1
|
Cribb DM, Moffatt CRM, Wallace RL, McLure AT, Bulach D, Jennison AV, French N, Valcanis M, Glass K, Kirk MD. Genomic and clinical characteristics of campylobacteriosis in Australia. Microb Genom 2024; 10:001174. [PMID: 38214338 PMCID: PMC10868609 DOI: 10.1099/mgen.0.001174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Accepted: 12/18/2023] [Indexed: 01/13/2024] Open
Abstract
Campylobacter spp. are a common cause of bacterial gastroenteritis in Australia, primarily acquired from contaminated meat. We investigated the relationship between genomic virulence characteristics and the severity of campylobacteriosis, hospitalisation, and other host factors.We recruited 571 campylobacteriosis cases from three Australian states and territories (2018-2019). We collected demographic, health status, risk factors, and self-reported disease data. We whole genome sequenced 422 C. jejuni and 84 C. coli case isolates along with 616 retail meat isolates. We classified case illness severity using a modified Vesikari scoring system, performed phylogenomic analysis, and explored risk factors for hospitalisation and illness severity.On average, cases experienced a 7.5 day diarrhoeal illness with additional symptoms including stomach cramps (87.1 %), fever (75.6 %), and nausea (72.0 %). Cases aged ≥75 years had milder symptoms, lower Vesikari scores, and higher odds of hospitalisation compared to younger cases. Chronic gastrointestinal illnesses also increased odds of hospitalisation. We observed significant diversity among isolates, with 65 C. jejuni and 21 C. coli sequence types. Antimicrobial resistance genes were detected in 20.4 % of isolates, but multidrug resistance was rare (0.04 %). Key virulence genes such as cdtABC (C. jejuni) and cadF were prevalent (>90 % presence) but did not correlate with disease severity or hospitalisation. However, certain genes (e.g. fliK, Cj1136, and Cj1138) appeared to distinguish human C. jejuni cases from food source isolates.Campylobacteriosis generally presents similarly across cases, though some are more severe. Genotypic virulence factors identified in the literature to-date do not predict disease severity but may differentiate human C. jejuni cases from food source isolates. Host factors like age and comorbidities have a greater influence on health outcomes than virulence factors.
Collapse
Affiliation(s)
- Danielle M. Cribb
- National Centre for Epidemiology and Population Health, the Australian National University, Canberra, Australia
| | - Cameron R. M. Moffatt
- Queensland Health Forensic and Scientific Services, Coopers Plains, Brisbane, Australia
| | - Rhiannon L. Wallace
- Agriculture and Agri-Food Canada, Agassiz Research and Development Centre, Agassiz, British Columbia, Canada
| | - Angus T. McLure
- National Centre for Epidemiology and Population Health, the Australian National University, Canberra, Australia
| | - Dieter Bulach
- Melbourne Bioinformatics, The University of Melbourne, Melbourne, Australia
- Microbiological Diagnostic Unit Public Health Laboratory, The Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Australia
| | - Amy V. Jennison
- Queensland Health Forensic and Scientific Services, Coopers Plains, Brisbane, Australia
| | - Nigel French
- Tāwharau Ora|School of Veterinary Science, Massey University, Palmerston North, New Zealand
| | - Mary Valcanis
- Microbiological Diagnostic Unit Public Health Laboratory, The Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Australia
| | - Kathryn Glass
- National Centre for Epidemiology and Population Health, the Australian National University, Canberra, Australia
| | - Martyn D. Kirk
- National Centre for Epidemiology and Population Health, the Australian National University, Canberra, Australia
| |
Collapse
|
2
|
McLure A, Smith JJ, Firestone SM, Kirk MD, French N, Fearnley E, Wallace R, Valcanis M, Bulach D, Moffatt CRM, Selvey LA, Jennison A, Cribb DM, Glass K. Source attribution of campylobacteriosis in Australia, 2017-2019. Risk Anal 2023; 43:2527-2548. [PMID: 37032319 PMCID: PMC10947381 DOI: 10.1111/risa.14138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 02/02/2023] [Accepted: 02/09/2023] [Indexed: 06/19/2023]
Abstract
Campylobacter jejuni and Campylobacter coli infections are the leading cause of foodborne gastroenteritis in high-income countries. Campylobacter colonizes a variety of warm-blooded hosts that are reservoirs for human campylobacteriosis. The proportions of Australian cases attributable to different animal reservoirs are unknown but can be estimated by comparing the frequency of different sequence types in cases and reservoirs. Campylobacter isolates were obtained from notified human cases and raw meat and offal from the major livestock in Australia between 2017 and 2019. Isolates were typed using multi-locus sequence genotyping. We used Bayesian source attribution models including the asymmetric island model, the modified Hald model, and their generalizations. Some models included an "unsampled" source to estimate the proportion of cases attributable to wild, feral, or domestic animal reservoirs not sampled in our study. Model fits were compared using the Watanabe-Akaike information criterion. We included 612 food and 710 human case isolates. The best fitting models attributed >80% of Campylobacter cases to chickens, with a greater proportion of C. coli (>84%) than C. jejuni (>77%). The best fitting model that included an unsampled source attributed 14% (95% credible interval [CrI]: 0.3%-32%) to the unsampled source and only 2% to ruminants (95% CrI: 0.3%-12%) and 2% to pigs (95% CrI: 0.2%-11%) The best fitting model that did not include an unsampled source attributed 12% to ruminants (95% CrI: 1.3%-33%) and 6% to pigs (95% CrI: 1.1%-19%). Chickens were the leading source of human Campylobacter infections in Australia in 2017-2019 and should remain the focus of interventions to reduce burden.
Collapse
Affiliation(s)
- Angus McLure
- National Centre for Epidemiology and Population HealthThe Australian National UniversityCanberraAustralia
| | - James J. Smith
- Food Safety Standards and Regulation, Health Protection BranchQueensland HealthBrisbaneAustralia
- School of Biology and Environmental Science, Faculty of ScienceQueensland University of TechnologyBrisbaneAustralia
| | - Simon Matthew Firestone
- Melbourne Veterinary School, Faculty of ScienceThe University of MelbourneMelbourneAustralia
| | - Martyn D. Kirk
- National Centre for Epidemiology and Population HealthThe Australian National UniversityCanberraAustralia
| | - Nigel French
- Infectious Disease Research Centre, Hopkirk Research InstituteMassey UniversityPalmerston NorthNew Zealand
- New Zealand Food Safety Science and Research Centre, Hopkirk Research InstituteMassey UniversityPalmerston NorthNew Zealand
| | - Emily Fearnley
- Department for Health and WellbeingGovernment of South AustraliaAdelaideAustralia
| | - Rhiannon Wallace
- Agassiz Research and Development Centre, Agriculture and Agri‐Food CanadaAgassizCanada
| | - Mary Valcanis
- The Doherty Institute for Infection and ImmunityMelbourneAustralia
- Microbiological Diagnostic Unit Public Health LaboratoryThe University of MelbourneMelbourneAustralia
| | - Dieter Bulach
- The Doherty Institute for Infection and ImmunityMelbourneAustralia
- Melbourne BioinformaticsThe University of MelbourneMelbourneAustralia
| | - Cameron R. M. Moffatt
- National Centre for Epidemiology and Population HealthThe Australian National UniversityCanberraAustralia
| | - Linda A. Selvey
- School of Public Health, Faculty of MedicineThe University of QueenslandBrisbaneAustralia
| | - Amy Jennison
- Public Health Microbiology, Forensic and Scientific Services, Queensland HealthBrisbaneAustralia
| | - Danielle M. Cribb
- National Centre for Epidemiology and Population HealthThe Australian National UniversityCanberraAustralia
| | - Kathryn Glass
- National Centre for Epidemiology and Population HealthThe Australian National UniversityCanberraAustralia
| |
Collapse
|
3
|
Carey ME, Dyson ZA, Ingle DJ, Amir A, Aworh MK, Chattaway MA, Chew KL, Crump JA, Feasey NA, Howden BP, Keddy KH, Maes M, Parry CM, Van Puyvelde S, Webb HE, Afolayan AO, Alexander AP, Anandan S, Andrews JR, Ashton PM, Basnyat B, Bavdekar A, Bogoch II, Clemens JD, da Silva KE, De A, de Ligt J, Diaz Guevara PL, Dolecek C, Dutta S, Ehlers MM, Francois Watkins L, Garrett DO, Godbole G, Gordon MA, Greenhill AR, Griffin C, Gupta M, Hendriksen RS, Heyderman RS, Hooda Y, Hormazabal JC, Ikhimiukor OO, Iqbal J, Jacob JJ, Jenkins C, Jinka DR, John J, Kang G, Kanteh A, Kapil A, Karkey A, Kariuki S, Kingsley RA, Koshy RM, Lauer AC, Levine MM, Lingegowda RK, Luby SP, Mackenzie GA, Mashe T, Msefula C, Mutreja A, Nagaraj G, Nagaraj S, Nair S, Naseri TK, Nimarota-Brown S, Njamkepo E, Okeke IN, Perumal SPB, Pollard AJ, Pragasam AK, Qadri F, Qamar FN, Rahman SIA, Rambocus SD, Rasko DA, Ray P, Robins-Browne R, Rongsen-Chandola T, Rutanga JP, Saha SK, Saha S, Saigal K, Sajib MSI, Seidman JC, Shakya J, Shamanna V, Shastri J, Shrestha R, Sia S, Sikorski MJ, Singh A, Smith AM, Tagg KA, Tamrakar D, Tanmoy AM, Thomas M, Thomas MS, Thomsen R, Thomson NR, Tupua S, Vaidya K, Valcanis M, Veeraraghavan B, Weill FX, Wright J, Dougan G, Argimón S, Keane JA, Aanensen DM, Baker S, Holt KE. Global diversity and antimicrobial resistance of typhoid fever pathogens: Insights from a meta-analysis of 13,000 Salmonella Typhi genomes. eLife 2023; 12:e85867. [PMID: 37697804 PMCID: PMC10506625 DOI: 10.7554/elife.85867] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Accepted: 08/02/2023] [Indexed: 09/13/2023] Open
Abstract
Background The Global Typhoid Genomics Consortium was established to bring together the typhoid research community to aggregate and analyse Salmonella enterica serovar Typhi (Typhi) genomic data to inform public health action. This analysis, which marks 22 years since the publication of the first Typhi genome, represents the largest Typhi genome sequence collection to date (n=13,000). Methods This is a meta-analysis of global genotype and antimicrobial resistance (AMR) determinants extracted from previously sequenced genome data and analysed using consistent methods implemented in open analysis platforms GenoTyphi and Pathogenwatch. Results Compared with previous global snapshots, the data highlight that genotype 4.3.1 (H58) has not spread beyond Asia and Eastern/Southern Africa; in other regions, distinct genotypes dominate and have independently evolved AMR. Data gaps remain in many parts of the world, and we show the potential of travel-associated sequences to provide informal 'sentinel' surveillance for such locations. The data indicate that ciprofloxacin non-susceptibility (>1 resistance determinant) is widespread across geographies and genotypes, with high-level ciprofloxacin resistance (≥3 determinants) reaching 20% prevalence in South Asia. Extensively drug-resistant (XDR) typhoid has become dominant in Pakistan (70% in 2020) but has not yet become established elsewhere. Ceftriaxone resistance has emerged in eight non-XDR genotypes, including a ciprofloxacin-resistant lineage (4.3.1.2.1) in India. Azithromycin resistance mutations were detected at low prevalence in South Asia, including in two common ciprofloxacin-resistant genotypes. Conclusions The consortium's aim is to encourage continued data sharing and collaboration to monitor the emergence and global spread of AMR Typhi, and to inform decision-making around the introduction of typhoid conjugate vaccines (TCVs) and other prevention and control strategies. Funding No specific funding was awarded for this meta-analysis. Coordinators were supported by fellowships from the European Union (ZAD received funding from the European Union's Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie grant agreement No 845681), the Wellcome Trust (SB, Wellcome Trust Senior Fellowship), and the National Health and Medical Research Council (DJI is supported by an NHMRC Investigator Grant [GNT1195210]).
Collapse
Affiliation(s)
- Megan E Carey
- Cambridge Institute of Therapeutic Immunology and Infectious Disease (CITIID), University of Cambridge School of Clinical Medicine, Cambridge Biomedical CampusCambridgeUnited Kingdom
- Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical MedicineLondonUnited Kingdom
- IAVI, Chelsea & Westminster HospitalLondonUnited Kingdom
| | - Zoe A Dyson
- Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical MedicineLondonUnited Kingdom
- Department of Infectious Diseases, Central Clinical School, Monash UniversityMelbourneAustralia
- Wellcome Sanger Institute, Wellcome Genome CampusHinxtonUnited Kingdom
| | - Danielle J Ingle
- Department of Microbiology and Immunology at the Peter Doherty Institute for Infection and Immunity, The University of MelbourneMelbourneAustralia
| | | | - Mabel K Aworh
- Nigeria Field Epidemiology and Laboratory Training ProgrammeAbujaNigeria
- College of Veterinary Medicine, North Carolina State UniversityRaleighUnited States
| | | | - Ka Lip Chew
- National University HospitalSingaporeSingapore
| | - John A Crump
- Centre for International Health, University of OtagoDunedinNew Zealand
| | - Nicholas A Feasey
- Department of Clinical Sciences, Liverpool School of Tropical MedicineLiverpoolUnited Kingdom
- Malawi-Liverpool Wellcome Programme, Kamuzu University of Health SciencesBlantyreMalawi
| | - Benjamin P Howden
- Centre for Pathogen Genomics, Department of Microbiology and Immunology, University of Melbourne at Doherty Institute for Infection and ImmunityMelbourneAustralia
- Microbiological Diagnostic Unit Public Health Laboratory, The University of Melbourne at the Peter Doherty Institute for Infection and ImmunityMelbourneAustralia
| | | | - Mailis Maes
- Cambridge Institute of Therapeutic Immunology and Infectious Disease (CITIID), University of Cambridge School of Clinical Medicine, Cambridge Biomedical CampusCambridgeUnited Kingdom
| | - Christopher M Parry
- Department of Clinical Sciences, Liverpool School of Tropical MedicineLiverpoolUnited Kingdom
| | - Sandra Van Puyvelde
- Cambridge Institute of Therapeutic Immunology and Infectious Disease (CITIID), University of Cambridge School of Clinical Medicine, Cambridge Biomedical CampusCambridgeUnited Kingdom
- University of AntwerpAntwerpBelgium
| | - Hattie E Webb
- Centers for Disease Control and PreventionAtlantaUnited States
| | - Ayorinde Oluwatobiloba Afolayan
- Global Health Research Unit (GHRU) for the Genomic Surveillance of Antimicrobial Resistance, Faculty of Pharmacy, University of IbadanIbadanNigeria
| | | | - Shalini Anandan
- Department of Clinical Microbiology, Christian Medical CollegeVelloreIndia
| | - Jason R Andrews
- Division of Infectious Diseases and Geographic Medicine, Stanford UniversityStanfordUnited States
| | - Philip M Ashton
- Malawi-Liverpool Wellcome ProgrammeBlantyreMalawi
- Institute of Infection, Veterinary and Ecological Sciences, University of LiverpoolLiverpoolUnited Kingdom
| | - Buddha Basnyat
- Oxford University Clinical Research Unit NepalKathmanduNepal
| | | | - Isaac I Bogoch
- Department of Medicine, Division of Infectious Diseases, University of TorontoTorontoCanada
| | - John D Clemens
- International Vaccine InstituteSeoulRepublic of Korea
- International Centre for Diarrhoeal Disease ResearchDhakaBangladesh
- UCLA Fielding School of Public HealthLos AngelesUnited States
- Korea UniversitySeoulRepublic of Korea
| | - Kesia Esther da Silva
- Division of Infectious Diseases and Geographic Medicine, Stanford UniversityStanfordUnited States
| | - Anuradha De
- Topiwala National Medical CollegeMumbaiIndia
| | - Joep de Ligt
- ESR, Institute of Environmental Science and Research Ltd., PoriruaWellingtonNew Zealand
| | | | - Christiane Dolecek
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of OxfordOxfordUnited Kingdom
- Mahidol Oxford Tropical Medicine Research Unit, Mahidol UniversityBangkokThailand
| | - Shanta Dutta
- ICMR - National Institute of Cholera & Enteric DiseasesKolkataIndia
| | - Marthie M Ehlers
- Department of Medical Microbiology, Faculty of Health Sciences, University of PretoriaPretoriaSouth Africa
- Department of Medical Microbiology, Tshwane Academic Division, National Health Laboratory ServicePretoriaSouth Africa
| | | | | | - Gauri Godbole
- United Kingdom Health Security AgencyLondonUnited Kingdom
| | - Melita A Gordon
- Institute of Infection, Veterinary and Ecological Sciences, University of LiverpoolLiverpoolUnited Kingdom
| | - Andrew R Greenhill
- Federation University AustraliaChurchillAustralia
- Papua New Guinea Institute of Medical ResearchGorokaPapua New Guinea
| | - Chelsey Griffin
- Centers for Disease Control and PreventionAtlantaUnited States
| | - Madhu Gupta
- Post Graduate Institute of Medical Education and ResearchChandigarhIndia
| | | | - Robert S Heyderman
- Research Department of Infection, Division of Infection and Immunity, University College LondonLondonUnited Kingdom
| | | | - Juan Carlos Hormazabal
- Bacteriologia, Subdepartamento de Enfermedades Infecciosas, Departamento de Laboratorio Biomedico, Instituto de Salud Publica de Chile (ISP)SantiagoChile
| | - Odion O Ikhimiukor
- Global Health Research Unit (GHRU) for the Genomic Surveillance of Antimicrobial Resistance, Faculty of Pharmacy, University of IbadanIbadanNigeria
| | - Junaid Iqbal
- Department of Pediatrics and Child Health, Aga Khan UniversityKarachiPakistan
| | - Jobin John Jacob
- Department of Clinical Microbiology, Christian Medical CollegeVelloreIndia
| | - Claire Jenkins
- United Kingdom Health Security AgencyLondonUnited Kingdom
| | | | - Jacob John
- Department of Community Health, Christian Medical CollegeVelloreIndia
| | - Gagandeep Kang
- Department of Community Health, Christian Medical CollegeVelloreIndia
| | - Abdoulie Kanteh
- Medical Research Council Unit The Gambia at London School Hygiene & Tropical MedicineFajaraGambia
| | - Arti Kapil
- All India Institute of Medical SciencesDelhiIndia
| | | | - Samuel Kariuki
- Centre for Microbiology Research, Kenya Medical Research InstituteNairobiKenya
| | | | | | - AC Lauer
- Centers for Disease Control and PreventionAtlantaUnited States
| | - Myron M Levine
- Center for Vaccine Development and Global Health (CVD), University of Maryland School of Medicine, Baltimore, Maryland, USABaltimoreUnited States
| | | | - Stephen P Luby
- Division of Infectious Diseases and Geographic Medicine, Stanford UniversityStanfordUnited States
| | - Grant Austin Mackenzie
- Medical Research Council Unit The Gambia at London School Hygiene & Tropical MedicineFajaraGambia
| | - Tapfumanei Mashe
- National Microbiology Reference LaboratoryHarareZimbabwe
- World Health OrganizationHarareZimbabwe
| | | | - Ankur Mutreja
- Cambridge Institute of Therapeutic Immunology and Infectious Disease (CITIID), University of Cambridge School of Clinical Medicine, Cambridge Biomedical CampusCambridgeUnited Kingdom
| | - Geetha Nagaraj
- Central Research Laboratory, Kempegowda Institute of Medical SciencesBengaluruIndia
| | | | - Satheesh Nair
- United Kingdom Health Security AgencyLondonUnited Kingdom
| | | | | | | | - Iruka N Okeke
- Global Health Research Unit (GHRU) for the Genomic Surveillance of Antimicrobial Resistance, Faculty of Pharmacy, University of IbadanIbadanNigeria
| | | | - Andrew J Pollard
- Oxford Vaccine Group, Department of Paediatrics, University of OxfordOxfordUnited Kingdom
- The NIHR Oxford Biomedical Research CentreOxfordUnited Kingdom
| | | | - Firdausi Qadri
- International Centre for Diarrhoeal Disease ResearchDhakaBangladesh
| | - Farah N Qamar
- Department of Pediatrics and Child Health, Aga Khan UniversityKarachiPakistan
| | | | - Savitra Devi Rambocus
- Microbiological Diagnostic Unit Public Health Laboratory, The University of Melbourne at the Peter Doherty Institute for Infection and ImmunityMelbourneAustralia
| | - David A Rasko
- Department of Microbiology and Immunology, University of Maryland School of MedicineBaltimoreUnited States
- Institute for Genome Sciences, University of Maryland School of MedicineBaltimoreUnited States
| | - Pallab Ray
- Post Graduate Institute of Medical Education and ResearchChandigarhIndia
| | - Roy Robins-Browne
- Department of Microbiology and Immunology at the Peter Doherty Institute for Infection and Immunity, The University of MelbourneMelbourneAustralia
- Murdoch Children’s Research Institute, Royal Children’s HospitalParkvilleAustralia
| | | | | | | | | | | | - Mohammad Saiful Islam Sajib
- Child Health Research FoundationDhakaBangladesh
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of GlasgowGlasgowUnited Kingdom
| | | | - Jivan Shakya
- Dhulikhel HospitalDhulikhelNepal
- Institute for Research in Science and TechnologyKathmanduNepal
| | - Varun Shamanna
- Central Research Laboratory, Kempegowda Institute of Medical SciencesBengaluruIndia
| | - Jayanthi Shastri
- Topiwala National Medical CollegeMumbaiIndia
- Kasturba Hospital for Infectious DiseasesMumbaiIndia
| | - Rajeev Shrestha
- Center for Infectious Disease Research & Surveillance, Dhulikhel Hospital, Kathmandu University HospitalDhulikhelNepal
| | - Sonia Sia
- Research Institute for Tropical Medicine, Department of HealthMuntinlupa CityPhilippines
| | - Michael J Sikorski
- Center for Vaccine Development and Global Health (CVD), University of Maryland School of Medicine, Baltimore, Maryland, USABaltimoreUnited States
- Department of Microbiology and Immunology, University of Maryland School of MedicineBaltimoreUnited States
- Institute for Genome Sciences, University of Maryland School of MedicineBaltimoreUnited States
| | | | - Anthony M Smith
- Centre for Enteric Diseases, National Institute for Communicable DiseasesJohannesburgSouth Africa
| | - Kaitlin A Tagg
- Centers for Disease Control and PreventionAtlantaUnited States
| | - Dipesh Tamrakar
- Center for Infectious Disease Research & Surveillance, Dhulikhel Hospital, Kathmandu University HospitalDhulikhelNepal
| | | | - Maria Thomas
- Christian Medical College, LudhianaLudhianaIndia
| | | | | | | | - Siaosi Tupua
- Ministry of Health, Government of SamoaApiaSamoa
| | | | - Mary Valcanis
- Microbiological Diagnostic Unit Public Health Laboratory, The University of Melbourne at the Peter Doherty Institute for Infection and ImmunityMelbourneAustralia
| | | | | | - Jackie Wright
- ESR, Institute of Environmental Science and Research Ltd., PoriruaWellingtonNew Zealand
| | - Gordon Dougan
- Cambridge Institute of Therapeutic Immunology and Infectious Disease (CITIID), University of Cambridge School of Clinical Medicine, Cambridge Biomedical CampusCambridgeUnited Kingdom
| | - Silvia Argimón
- Centre for Genomic Pathogen Surveillance, Big Data Institute, University of OxfordOxfordUnited Kingdom
| | - Jacqueline A Keane
- Cambridge Institute of Therapeutic Immunology and Infectious Disease (CITIID), University of Cambridge School of Clinical Medicine, Cambridge Biomedical CampusCambridgeUnited Kingdom
| | - David M Aanensen
- Centre for Genomic Pathogen Surveillance, Big Data Institute, University of OxfordOxfordUnited Kingdom
| | - Stephen Baker
- Cambridge Institute of Therapeutic Immunology and Infectious Disease (CITIID), University of Cambridge School of Clinical Medicine, Cambridge Biomedical CampusCambridgeUnited Kingdom
- IAVI, Chelsea & Westminster HospitalLondonUnited Kingdom
| | - Kathryn E Holt
- Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical MedicineLondonUnited Kingdom
- Department of Infectious Diseases, Central Clinical School, Monash UniversityMelbourneAustralia
| |
Collapse
|
4
|
Kiss C, Kotsanas D, Francis MJ, Sait M, Valcanis M, Lacey J, Connelly K, Rogers B, Ballard SA, Howden BP, Graham M. Molecular epidemiology, clinical features and significance of Shiga toxin detection from routine testing of gastroenteritis specimens. Pathology 2023:S0031-3025(23)00119-8. [PMID: 37271611 DOI: 10.1016/j.pathol.2023.03.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Revised: 02/20/2023] [Accepted: 03/07/2023] [Indexed: 06/06/2023]
Abstract
After introduction of faecal multiplex PCR that includes targets for stx1 and stx2 genes, we found stx genes were detected in 120 specimens from 111 patients over a 31-month period from 2018-2020 from a total of 14,179 separate tests performed. The proportion of stx1 only vs stx2 only vs stx1 and stx2 was 35%, 22% and 42%, respectively. There were 54 specimens which were culture positive, with 33 different serotypes identified, the predominant serotype being O157:H7 (19%). Eighty-two patients had clinical data available; we found a high rate of fever (35%), bloody diarrhoea (34%), acute kidney injury (27%), hospital admission (80%) and detection of faecal co-pathogens (23%). Only one patient developed haemolytic uraemic syndrome. We found no significant association with stx genotype and any particular symptom or complication. We found a significant association of serotypes O157:H7 and O26:H11 with bloody stool, but no significant association with any other symptom or complication.
Collapse
Affiliation(s)
- Christopher Kiss
- Department of Microbiology, Monash Health, Clayton, Vic, Australia.
| | - Despina Kotsanas
- Monash Infectious Diseases, Monash Health, Clayton, Vic, Australia
| | | | - Michelle Sait
- Microbiological Diagnostic Unit Public Health Laboratory, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Vic, Australia
| | - Mary Valcanis
- Microbiological Diagnostic Unit Public Health Laboratory, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Vic, Australia
| | - Jake Lacey
- Microbiological Diagnostic Unit Public Health Laboratory, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Vic, Australia
| | - Kathryn Connelly
- Faculty of Medicine Nursing and Health Sciences, Monash University, Clayton, Vic, Australia; Monash University School of Clinical Sciences, Monash Health, Clayton, Vic, Australia
| | - Benjamin Rogers
- Monash Infectious Diseases, Monash Health, Clayton, Vic, Australia; Faculty of Medicine Nursing and Health Sciences, Monash University, Clayton, Vic, Australia
| | - Susan A Ballard
- Microbiological Diagnostic Unit Public Health Laboratory, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Vic, Australia
| | - Benjamin P Howden
- Microbiological Diagnostic Unit Public Health Laboratory, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Vic, Australia; Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Vic, Australia
| | - Maryza Graham
- Department of Microbiology, Monash Health, Clayton, Vic, Australia; Monash Infectious Diseases, Monash Health, Clayton, Vic, Australia; Microbiological Diagnostic Unit Public Health Laboratory, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Vic, Australia; Faculty of Medicine Nursing and Health Sciences, Monash University, Clayton, Vic, Australia
| |
Collapse
|
5
|
Parker EM, Valcanis M, Andersson P, Wittum TE. Investigating the Source of Salmonella Agona Contamination in Australian Feed Mills Using Core Genome Phylogenetic Analysis. Foodborne Pathog Dis 2023; 20:132-137. [PMID: 37062813 DOI: 10.1089/fpd.2022.0066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/18/2023] Open
Abstract
Salmonella enterica serovar Agona is commonly detected in raw animal feed components during routine microbial monitoring of Australian commercial animal feed mills. We hypothesized that Salmonella-contaminated raw feed components originate at the rendering or oil seed crushing plant and are distributed to mills in different locations. Our objective was to investigate the source of Salmonella Agona contaminated raw feed components. Whole genome sequences of 37 Salmonella Agona isolates, 36 from raw feed components and 1 from finished feed, collected from 10 Australian feed mills located in 4 Australian states, were compared using core genome phylogenetic analysis. After DNA extraction and de novo draft assembly of the paired reads, the draft genomes were aligned using conserved signature indel phylogeny against a reference genome for Salmonella Agona, to identify single nucleotide polymorphisms in the core genome. Five distinct clades corresponding to the five different suppliers of Salmonella Agona-contaminated raw feed components were identified in the resulting phylogenetic tree. The results also provided evidence of cross-transference of Salmonella Agona between canola meal, meat meal, and finished feed within a mill. Core genome phylogenetic analysis facilitated tracing the source of Salmonella contamination in feed mills.
Collapse
Affiliation(s)
- Elizabeth Mary Parker
- The Department of Veterinary Preventive Medicine, The Ohio State University, Columbus, Ohio, USA
| | - Mary Valcanis
- Microbiological Diagnostic Unit-Public Health Laboratory, Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Australia
| | - Patiyan Andersson
- Microbiological Diagnostic Unit-Public Health Laboratory, Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Australia
| | - Thomas E Wittum
- The Department of Veterinary Preventive Medicine, The Ohio State University, Columbus, Ohio, USA
| |
Collapse
|
6
|
Morris JM, Mercoulia K, Valcanis M, Gorrie CL, Sherry NL, Howden BP. Hidden Resistances: How Routine Whole-Genome Sequencing Uncovered an Otherwise Undetected blaNDM-1 Gene in Vibrio alginolyticus from Imported Seafood. Microbiol Spectr 2023; 11:e0417622. [PMID: 36602387 PMCID: PMC9927303 DOI: 10.1128/spectrum.04176-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Accepted: 12/06/2022] [Indexed: 01/06/2023] Open
Abstract
Vibrio alginolyticus causes vibriosis of marine vertebrates, invertebrates, and humans, and while there have been several reports of multidrug resistance in V. alginolyticus, carbapenem resistance is rare. V. alginolyticus strain AUSMDU00064140 was isolated in Melbourne, Australia, from imported prawns. Routine genomic surveillance detected the presence of a full-length blaNDM-1 gene, subsequently shown to be collocated with additional acquired antimicrobial resistance genes on a resistance cassette on the largest chromosome, flanked by mobilization gene annotations. Comparisons to a previously described V. alginolyticus plasmid, pC1349, revealed differing gene content and arrangements between the resistance cassettes. Phylogenetic analysis was performed against a local and global data set (n = 109), demonstrating that AUSMDU00064140 was distinct and did not cluster with any other strains. Despite the presence of the complete blaNDM-1 gene and positive phenotypic assays for carbapenemase production, carbapenem MICs were low (meropenem MIC ≤0.5 mg/liter). However, it is still possible that this gene may be transferred to another species in the environment or a host, causing phenotypic carbapenem resistance and presenting a risk of great public health concern. IMPORTANCE Carbapenems are last-line antimicrobials, vital for use in human medicine. Antimicrobial resistance determinants such as blaNDM (New Delhi metallo-β-lactamase producing) genes conferring resistance to the carbapenem class of antimicrobials, are typically found in Enterobacterales (first described in 2009 from a Klebsiella pneumoniae isolate). Our study shows that Vibrio alginolyticus isolated from cooked prawn is able to harbor antimicrobial resistance (AMR) genes of public health concern, specifically a chromosomally located blaNDM-1 gene, and there is the potential for transmission of resistance genes. This may be linked with antimicrobial use in low- and middle-income settings, which has typically been high, unregulated, or not reported. Many countries, including Thailand, have implemented national strategic plans to incorporate the World Health Organization (WHO)'s Global Action Plan (2015) recommendations of a global One Health approach, including increased resources for surveillance of antimicrobial usage and AMR; however, efficient antimicrobial surveillance systems incorporating genomic and phenotypic testing of isolates are still lacking in many jurisdictions.
Collapse
Affiliation(s)
- Jacqueline M. Morris
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Karolina Mercoulia
- Microbiological Diagnostic Unit Public Health Laboratory, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Mary Valcanis
- Microbiological Diagnostic Unit Public Health Laboratory, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Claire L. Gorrie
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Norelle L. Sherry
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
- Microbiological Diagnostic Unit Public Health Laboratory, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Benjamin P. Howden
- Department of Microbiology and Immunology, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
- Microbiological Diagnostic Unit Public Health Laboratory, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| |
Collapse
|
7
|
Sherry NL, Horan KA, Ballard SA, Gonҫalves da Silva A, Gorrie CL, Schultz MB, Stevens K, Valcanis M, Sait ML, Stinear TP, Howden BP, Seemann T. An ISO-certified genomics workflow for identification and surveillance of antimicrobial resistance. Nat Commun 2023; 14:60. [PMID: 36599823 DOI: 10.1038/s41467-022-35713-4] [Citation(s) in RCA: 26] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Accepted: 12/21/2022] [Indexed: 01/05/2023] Open
Abstract
Realising the promise of genomics to revolutionise identification and surveillance of antimicrobial resistance (AMR) has been a long-standing challenge in clinical and public health microbiology. Here, we report the creation and validation of abritAMR, an ISO-certified bioinformatics platform for genomics-based bacterial AMR gene detection. The abritAMR platform utilises NCBI's AMRFinderPlus, as well as additional features that classify AMR determinants into antibiotic classes and provide customised reports. We validate abritAMR by comparing with PCR or reference genomes, representing 1500 different bacteria and 415 resistance alleles. In these analyses, abritAMR displays 99.9% accuracy, 97.9% sensitivity and 100% specificity. We also compared genomic predictions of phenotype for 864 Salmonella spp. against agar dilution results, showing 98.9% accuracy. The implementation of abritAMR in our institution has resulted in streamlined bioinformatics and reporting pathways, and has been readily updated and re-verified. The abritAMR tool and validation datasets are publicly available to assist laboratories everywhere harness the power of AMR genomics in professional practice.
Collapse
Affiliation(s)
- Norelle L Sherry
- Microbiological Diagnostic Unit Public Health Laboratory (MDU-PHL), Department of Microbiology & Immunology, University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, Victoria, Australia.,Department of Infectious Diseases, Austin Health, Heidelberg, Victoria, Australia.,Department of Microbiology & Immunology, University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, Australia
| | - Kristy A Horan
- Microbiological Diagnostic Unit Public Health Laboratory (MDU-PHL), Department of Microbiology & Immunology, University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, Victoria, Australia
| | - Susan A Ballard
- Microbiological Diagnostic Unit Public Health Laboratory (MDU-PHL), Department of Microbiology & Immunology, University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, Victoria, Australia
| | - Anders Gonҫalves da Silva
- Microbiological Diagnostic Unit Public Health Laboratory (MDU-PHL), Department of Microbiology & Immunology, University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, Victoria, Australia
| | - Claire L Gorrie
- Department of Microbiology & Immunology, University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, Australia
| | - Mark B Schultz
- Microbiological Diagnostic Unit Public Health Laboratory (MDU-PHL), Department of Microbiology & Immunology, University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, Victoria, Australia
| | - Kerrie Stevens
- Microbiological Diagnostic Unit Public Health Laboratory (MDU-PHL), Department of Microbiology & Immunology, University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, Victoria, Australia
| | - Mary Valcanis
- Microbiological Diagnostic Unit Public Health Laboratory (MDU-PHL), Department of Microbiology & Immunology, University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, Victoria, Australia
| | - Michelle L Sait
- Microbiological Diagnostic Unit Public Health Laboratory (MDU-PHL), Department of Microbiology & Immunology, University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, Victoria, Australia
| | - Timothy P Stinear
- Department of Microbiology & Immunology, University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, Australia
| | - Benjamin P Howden
- Microbiological Diagnostic Unit Public Health Laboratory (MDU-PHL), Department of Microbiology & Immunology, University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, Victoria, Australia. .,Department of Infectious Diseases, Austin Health, Heidelberg, Victoria, Australia. .,Department of Microbiology & Immunology, University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, Australia.
| | - Torsten Seemann
- Microbiological Diagnostic Unit Public Health Laboratory (MDU-PHL), Department of Microbiology & Immunology, University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, Victoria, Australia.,Department of Microbiology & Immunology, University of Melbourne at the Peter Doherty Institute for Infection & Immunity, Melbourne, Australia
| |
Collapse
|
8
|
Sikorski MJ, Ma J, Hazen TH, Desai SN, Tupua S, Nimarota-Brown S, Sialeipata M, Rambocus S, Ballard SA, Valcanis M, Thomsen RE, Robins-Browne RM, Howden BP, Naseri TK, Levine MM, Rasko DA. Spatial-temporal and phylogenetic analyses of epidemiologic data to help understand the modes of transmission of endemic typhoid fever in Samoa. PLoS Negl Trop Dis 2022; 16:e0010348. [PMID: 36251704 PMCID: PMC9612817 DOI: 10.1371/journal.pntd.0010348] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 10/27/2022] [Accepted: 09/15/2022] [Indexed: 11/05/2022] Open
Abstract
Salmonella enterica serovar Typhi (S. Typhi) is either widely distributed or proximally transmitted via fecally-contaminated food or water to cause typhoid fever. In Samoa, where endemic typhoid fever has persisted over decades despite water quality and sanitation improvements, the local patterns of S. Typhi circulation remain unclear. From April 2018-June 2020, epidemiologic data and GPS coordinates were collected during household investigations of 260 acute cases of typhoid fever, and 27 asymptomatic shedders of S. Typhi were detected among household contacts. Spatial and temporal distributions of cases were examined using Average Nearest Neighbor and space-time hotspot analyses. In rural regions, infections occurred in sporadic, focal clusters contrasting with persistent, less clustered cases in the Apia Urban Area. Restrictions to population movement during nationwide lockdowns in 2019-2020 were associated with marked reductions of cases. Phylogenetic analyses of isolates with whole genome sequences (n = 186) revealed one dominant genotype 3.5.4 (n = 181/186) that contains three Samoa-exclusive sub-lineages: 3.5.4.1, 3.5.4.2, and 3.5.4.3. Variables of patient sex, age, and geographic region were examined by phylogenetic groupings, and significant differences (p<0.05) associated genetically-similar isolates in urban areas with working ages (20-49 year olds), and in rural areas with age groups typically at home (<5, 50+). Isolates from asymptomatic shedders were among all three sub-lineages. Whole genome sequencing provided evidence of bacterial genetic similarity, which corroborated 10/12 putative epidemiologic linkages among cases and asymptomatic shedders, as well as 3/3 repeat positives (presumed relapses), with a median of one single nucleotide polymorphism difference. These findings highlight various patterns of typhoid transmission in Samoa that differ between urban and rural regions as well as genomic subtypes. Asymptomatic shedders, detectable only through household investigations, are likely an important reservoir and mobile agent of infection. This study advances a "Samoan S. Typhi framework" that supports current and future typhoid surveillance and control efforts in Samoa.
Collapse
Affiliation(s)
- Michael J. Sikorski
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, United States of America,Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, Maryland, United States of America,Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - Jianguo Ma
- Department of Geographical Sciences, University of Maryland, College Park, Maryland, United States of America
| | - Tracy H. Hazen
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, United States of America,Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - Sachin N. Desai
- Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - Siaosi Tupua
- Ministry of Health, Government of Samoa, Apia, Samoa
| | | | | | - Savitra Rambocus
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Susan A. Ballard
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Mary Valcanis
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | | | - Roy M. Robins-Browne
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia,Murdoch Children’s Research Institute, Royal Children’s Hospital, Parkville, Victoria, Australia
| | - Benjamin P. Howden
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | | | - Myron M. Levine
- Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, Maryland, United States of America,Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, Maryland, United States of America
| | - David A. Rasko
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, United States of America,Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, Maryland, United States of America,* E-mail:
| |
Collapse
|
9
|
Davies MR, Duchene S, Valcanis M, Jenkins AP, Jenney A, Rosa V, Hayes AJ, Strobel AG, McIntyre L, Lacey JA, Klemm EJ, Wong VK, Sahukhan A, Thomson H, Page A, Hocking D, Wang N, Tudravu L, Rafai E, Dougan G, Howden BP, Crump JA, Mulholland K, Strugnell RA. Genomic epidemiology of Salmonella Typhi in Central Division, Fiji, 2012 to 2016. Lancet Reg Health West Pac 2022; 24:100488. [PMID: 35769175 PMCID: PMC9234096 DOI: 10.1016/j.lanwpc.2022.100488] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
BACKGROUND Typhoid fever is endemic in some Pacific Island Countries including Fiji and Samoa yet genomic surveillance is not routine in such settings. Previous studies suggested imports of the global H58 clade of Salmonella enterica var Typhi (Salmonella Typhi) contribute to disease in these countries which, given the MDR potential of H58, does not auger well for treatment. The objective of the study was to define the genomic epidemiology of Salmonella Typhi in Fiji. METHODS Genomic sequencing approaches were implemented to study the distribution of 255 Salmonella Typhi isolates from the Central Division of Fiji. We augmented epidemiological surveillance and Bayesian phylogenomic approaches with a multi-year typhoid case-control study to define geospatial patterns among typhoid cases. FINDINGS Genomic analyses showed Salmonella Typhi from Fiji resolved into 2 non-H58 genotypes with isolates from the two dominant ethnic groups, the Indigenous (iTaukei) and non-iTaukei genetically indistinguishable. Low rates of international importation of clones was observed and overall, there were very low levels an antibiotic resistance within the endemic Fijian typhoid genotypes. Genomic epidemiological investigations were able to identify previously unlinked case clusters. Bayesian phylodynamic analyses suggested that genomic variation within the larger endemic Salmonella Typhi genotype expanded at discreet times, then contracted. INTERPRETATION Cyclones and flooding drove 'waves' of typhoid outbreaks in Fiji which, through population aggregation, poor sanitation and water safety, and then mobility of the population, spread clones more widely. Minimal international importations of new typhoid clones suggest that targeted local intervention strategies may be useful in controlling endemic typhoid infection. These findings add to our understanding of typhoid transmission networks in an endemic island country with broad implications, particularly across Pacific Island Countries. FUNDING This work was supported by the Coalition Against Typhoid through the Bill and Melinda Gates Foundation [grant number OPP1017518], the Victorian Government, the National Health and Medical Research Council Australia, the Australian Research Council, and the Fiji Ministry of Health and Medical Services.
Collapse
Affiliation(s)
- Mark R. Davies
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Victoria, Australia
| | - Sebastian Duchene
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Victoria, Australia
| | - Mary Valcanis
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Aaron P. Jenkins
- Centre for Ecosystem Management, Edith Cowan University, Western Australia
- School of Public Health, University of Sydney, Sydney, NSW, Australia
| | - Adam Jenney
- New Vaccines Group, Murdoch Children's Research Institute, Victoria, Australia
- College of Medicine, Nursing and Health Sciences, Fiji National University, Suva, Fiji
| | - Varanisese Rosa
- Fiji Centre for Disease Control, Fiji Ministry of Health, Suva, Fiji
| | - Andrew J. Hayes
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Victoria, Australia
| | - Aneley Getahun Strobel
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Victoria, Australia
| | - Liam McIntyre
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Victoria, Australia
| | - Jake A. Lacey
- Department of Infectious Diseases, The University of Melbourne at the Peter Doherty Institute of Infection and Immunity, Victoria, Australia
| | - Elizabeth J. Klemm
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Vanessa K. Wong
- Department of Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Aalisha Sahukhan
- Fiji Centre for Disease Control, Fiji Ministry of Health, Suva, Fiji
| | - Helen Thomson
- New Vaccines Group, Murdoch Children's Research Institute, Victoria, Australia
| | - Andrew Page
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
- Quadram Institute Bioscience, Norwich Research Park, Norfolk, United Kingdom
| | - Dianna Hocking
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Victoria, Australia
| | - Nancy Wang
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Victoria, Australia
| | | | - Eric Rafai
- Fiji Ministry of Health and Medical Services, Suva, Fiji
| | - Gordon Dougan
- Department of Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Benjamin P. Howden
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Victoria, Australia
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - John A. Crump
- Centre for International Health, Otago Medical School, University of Otago, Dunedin, New Zealand
| | - Kim Mulholland
- New Vaccines Group, Murdoch Children's Research Institute, Victoria, Australia
- Department of Infectious Disease Epidemiology, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Richard A. Strugnell
- Department of Microbiology and Immunology, The University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Victoria, Australia
| |
Collapse
|
10
|
Cribb DM, Varrone L, Wallace RL, McLure AT, Smith JJ, Stafford RJ, Bulach DM, Selvey LA, Firestone SM, French NP, Valcanis M, Fearnley EJ, Sloan-Gardner TS, Graham T, Glass K, Kirk MD. Risk factors for campylobacteriosis in Australia: outcomes of a 2018-2019 case-control study. BMC Infect Dis 2022; 22:586. [PMID: 35773664 PMCID: PMC9245254 DOI: 10.1186/s12879-022-07553-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Accepted: 06/09/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND We aimed to identify risk factors for sporadic campylobacteriosis in Australia, and to compare these for Campylobacter jejuni and Campylobacter coli infections. METHODS In a multi-jurisdictional case-control study, we recruited culture-confirmed cases of campylobacteriosis reported to state and territory health departments from February 2018 through October 2019. We recruited controls from notified influenza cases in the previous 12 months that were frequency matched to cases by age group, sex, and location. Campylobacter isolates were confirmed to species level by public health laboratories using molecular methods. We conducted backward stepwise multivariable logistic regression to identify significant risk factors. RESULTS We recruited 571 cases of campylobacteriosis (422 C. jejuni and 84 C. coli) and 586 controls. Important risk factors for campylobacteriosis included eating undercooked chicken (adjusted odds ratio [aOR] 70, 95% CI 13-1296) or cooked chicken (aOR 1.7, 95% CI 1.1-2.8), owning a pet dog aged < 6 months (aOR 6.4, 95% CI 3.4-12), and the regular use of proton-pump inhibitors in the 4 weeks prior to illness (aOR 2.8, 95% CI 1.9-4.3). Risk factors remained similar when analysed specifically for C. jejuni infection. Unique risks for C. coli infection included eating chicken pâté (aOR 6.1, 95% CI 1.5-25) and delicatessen meats (aOR 1.8, 95% CI 1.0-3.3). Eating any chicken carried a high population attributable fraction for campylobacteriosis of 42% (95% CI 13-68), while the attributable fraction for proton-pump inhibitors was 13% (95% CI 8.3-18) and owning a pet dog aged < 6 months was 9.6% (95% CI 6.5-13). The population attributable fractions for these variables were similar when analysed by campylobacter species. Eating delicatessen meats was attributed to 31% (95% CI 0.0-54) of cases for C. coli and eating chicken pâté was attributed to 6.0% (95% CI 0.0-11). CONCLUSIONS The main risk factor for campylobacteriosis in Australia is consumption of chicken meat. However, contact with young pet dogs may also be an important source of infection. Proton-pump inhibitors are likely to increase vulnerability to infection.
Collapse
Affiliation(s)
- Danielle M Cribb
- National Centre for Epidemiology and Population Health, The Australian National University, Canberra, ACT, Australia
| | - Liana Varrone
- Department of Health, Government of Western Australia, Perth, WA, Australia
| | - Rhiannon L Wallace
- Agriculture and Agri-Food Canada, Agassiz Research and Development Centre, Agassiz, BC, Canada
| | - Angus T McLure
- National Centre for Epidemiology and Population Health, The Australian National University, Canberra, ACT, Australia
| | - James J Smith
- Food Safety Standards and Regulation, Health Protection Branch, Queensland Health, Brisbane, Qld, Australia.,School of Biology and Environmental Science, Faculty of Science, Queensland University of Technology, Brisbane, Qld, Australia
| | - Russell J Stafford
- OzFoodNet, Communicable Diseases Branch, Queensland Health, Brisbane, Qld, Australia
| | - Dieter M Bulach
- Melbourne Bioinformatics, The University of Melbourne, Melbourne, Vic, Australia.,Microbiological Diagnostic Unit Public Health Laboratory, The Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Vic, Australia
| | - Linda A Selvey
- Faculty of Medicine, The University of Queensland, Brisbane, Qld, Australia
| | - Simon M Firestone
- Melbourne Veterinary School, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Vic, Australia
| | - Nigel P French
- Infectious Disease Research Centre, Massey University, Palmerston North, New Zealand
| | - Mary Valcanis
- Microbiological Diagnostic Unit Public Health Laboratory, The Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Vic, Australia
| | - Emily J Fearnley
- OzFoodNet, Government of South Australia, Department for Health and Wellbeing, Adelaide, SK, Australia
| | | | - Trudy Graham
- Public Health Microbiology, Forensic and Scientific Services, Queensland Health, Brisbane, Qld, Australia
| | - Kathryn Glass
- National Centre for Epidemiology and Population Health, The Australian National University, Canberra, ACT, Australia
| | - Martyn D Kirk
- National Centre for Epidemiology and Population Health, The Australian National University, Canberra, ACT, Australia.
| |
Collapse
|
11
|
Parker EM, Valcanis M, Edwards LJ, Andersson P, Mollenkopf DF, Wittum TE. Antimicrobial-resistant Salmonella is detected more frequently in feed milling equipment than in raw feed components or processed animal feed. Aust Vet J 2022; 100:213-219. [PMID: 35040117 PMCID: PMC9304270 DOI: 10.1111/avj.13146] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Revised: 01/04/2022] [Accepted: 01/06/2022] [Indexed: 11/30/2022]
Abstract
Food for human and animal consumption can provide a vehicle for the transfer of pathogenic and antimicrobial‐resistant bacteria into the food chain. We investigated the antimicrobial susceptibility of 453 Salmonella isolates collected from raw feed components, equipment and finished feed from 17 commercial feed mills in Australia between 2012 and 2021. Previous studies have found Salmonella prevalence and the diversity of Salmonella serotypes are greatest in the raw feed components. We, therefore, hypothesised that we would find a greater proportion of antimicrobial‐resistant Salmonella isolates in the raw feed components compared to other sample types. We found that of 453 isolates tested, 356 (0.80) were susceptible to all antimicrobials tested, 49 (0.11) were nonsusceptible to streptomycin only and 48 (0.11) were resistant to two or more antimicrobials. Of the 48 antimicrobial‐resistant isolates, 44 were found in feed milling equipment, two in raw feed components and two in finished feed. Statistical analysis, using a logistic regression with random effects model, found that the population‐adjusted mean probability of detecting antimicrobial‐resistant Salmonella isolates from feed milling equipment of 0.39, was larger than the probability of detecting resistant isolates in raw feed components 0.01, (P < 0.001) and in finished feed, 0.11, (P = 0.006). This propensity for antimicrobial‐resistant bacteria to colonise feed milling equipment has not been previously reported. Further studies are required to understand the ecology of antimicrobial‐resistant Salmonella in the feed milling environment.
Collapse
Affiliation(s)
- E M Parker
- The Department of Veterinary Preventive Medicine, The Ohio State University, 1920, Coffey Road, Columbus, Ohio, 43210, USA
| | - M Valcanis
- Microbiological Diagnostic Unit-Public Health Laboratory, Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
| | - L J Edwards
- Ridley AgriProducts Pty Ltd, 70-80, Bald Hill Road, Pakenham, Victoria, 3810, Australia
| | - P Andersson
- Microbiological Diagnostic Unit-Public Health Laboratory, Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
| | - D F Mollenkopf
- The Department of Veterinary Preventive Medicine, The Ohio State University, 1920, Coffey Road, Columbus, Ohio, 43210, USA
| | - T E Wittum
- The Department of Veterinary Preventive Medicine, The Ohio State University, 1920, Coffey Road, Columbus, Ohio, 43210, USA
| |
Collapse
|
12
|
Sim EM, Kim R, Gall M, Arnott A, Howard P, Valcanis M, Howden BP, Sintchenko V. Added Value of Genomic Surveillance of Virulence Factors in Shiga Toxin-Producing Escherichia coli in New South Wales, Australia. Front Microbiol 2022; 12:713724. [PMID: 35002991 PMCID: PMC8733641 DOI: 10.3389/fmicb.2021.713724] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Accepted: 11/22/2021] [Indexed: 11/25/2022] Open
Abstract
The disease caused by Shiga toxin-producing Escherichia coli (STEC) remains a significant public health challenge globally, but the incidence of human STEC infections in Australia remains relatively low. This study examined the virulence characteristics and diversity of STEC isolates in the state of New South Wales between December 2017 and May 2020. Utilisation of both whole and core genome multi-locus sequence typing (MLST) allowed for the inference of genomic diversity and detection of isolates that were likely to be epidemiologically linked. The most common STEC serotype and stx subtype detected in this study were O157:H7 and stx1a, respectively. A genomic scan of other virulence factors present in STEC suggested interplay between iron uptake system and virulence factors that mediate either iron release or countermeasures against host defence that could result in a reduction of stx1a expression. This reduced expression of the dominant stx genotype could contribute to the reduced incidence of STEC-related illness in Australia. Genomic surveillance of STEC becomes an important part of public health response and ongoing interrogation of virulence factors in STEC offers additional insights for the public health risk assessment.
Collapse
Affiliation(s)
- Eby M Sim
- Enteric Reference Laboratory and Microbial Genomics Laboratory, Centre for Infectious Diseases and Microbiology Laboratory Services, NSW Health Pathology, Institute of Clinical Pathology and Medical Research, Westmead, NSW, Australia
| | - Ryan Kim
- Enteric Reference Laboratory and Microbial Genomics Laboratory, Centre for Infectious Diseases and Microbiology Laboratory Services, NSW Health Pathology, Institute of Clinical Pathology and Medical Research, Westmead, NSW, Australia
| | - Mailie Gall
- Enteric Reference Laboratory and Microbial Genomics Laboratory, Centre for Infectious Diseases and Microbiology Laboratory Services, NSW Health Pathology, Institute of Clinical Pathology and Medical Research, Westmead, NSW, Australia
| | - Alicia Arnott
- Enteric Reference Laboratory and Microbial Genomics Laboratory, Centre for Infectious Diseases and Microbiology Laboratory Services, NSW Health Pathology, Institute of Clinical Pathology and Medical Research, Westmead, NSW, Australia
| | - Peter Howard
- Enteric Reference Laboratory and Microbial Genomics Laboratory, Centre for Infectious Diseases and Microbiology Laboratory Services, NSW Health Pathology, Institute of Clinical Pathology and Medical Research, Westmead, NSW, Australia
| | - Mary Valcanis
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, VIC, Australia
| | - Benjamin P Howden
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, VIC, Australia
| | - Vitali Sintchenko
- Enteric Reference Laboratory and Microbial Genomics Laboratory, Centre for Infectious Diseases and Microbiology Laboratory Services, NSW Health Pathology, Institute of Clinical Pathology and Medical Research, Westmead, NSW, Australia.,Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Sydney, NSW, Australia.,Centre for Infectious Diseases and Microbiology-Public Health, Westmead Hospital, Westmead, NSW, Australia
| |
Collapse
|
13
|
Kerr EJ, Stafford R, Rathnayake IU, Graham RMA, Fearnley E, Gregory J, Glasgow K, Wright R, Sintchenko V, Wang Q, Howard P, Leong LEX, Valcanis M, Pitchers W, Lambert SB, Jennison AV. Multistate Outbreak of Salmonella enterica Serovar Heidelberg with Unidentified Source, Australia, 2018-2019. Emerg Infect Dis 2022; 28:238-241. [PMID: 34932458 PMCID: PMC8714228 DOI: 10.3201/eid2801.211462] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
We report a multistate Salmonella enterica serovar Heidelberg outbreak in Australia during 2018-2019. Laboratory investigation of cases reported across 5 jurisdictions over a 7-month period could not identify a source of infection but detected indicators of severity and invasiveness. The hospitalization rate of 36% suggested a moderately severe clinical picture.
Collapse
|
14
|
Sia CM, Baines SL, Valcanis M, Lee DYJ, Gonçalves da Silva A, Ballard SA, Easton M, Seemann T, Howden BP, Ingle DJ, Williamson DA. Genomic diversity of antimicrobial resistance in non-typhoidal Salmonella in Victoria, Australia. Microb Genom 2021; 7:000725. [PMID: 34907895 PMCID: PMC8767345 DOI: 10.1099/mgen.0.000725] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Non-typhoidal Salmonella (NTS) is the second most common cause of foodborne bacterial gastroenteritis in Australia with antimicrobial resistance (AMR) increasing in recent years. Whole-genome sequencing (WGS) provides opportunities for in silico detection of AMR determinants. The objectives of this study were two-fold: (1) establish the utility of WGS analyses for inferring phenotypic resistance in NTS, and (2) explore clinically relevant genotypic AMR profiles to third generation cephalosporins (3GC) in NTS lineages. The concordance of 2490 NTS isolates with matched WGS and phenotypic susceptibility data against 13 clinically relevant antimicrobials was explored. In silico serovar prediction and typing was performed on assembled reads and interrogated for known AMR determinants. The surrounding genomic context, plasmid determinants and co-occurring AMR patterns were further investigated for multidrug resistant serovars harbouring blaCMY-2, blaCTX-M-55 or blaCTX-M-65. Our data demonstrated a high correlation between WGS and phenotypic susceptibility testing. Phenotypic-genotypic concordance was observed between 2440/2490 (98.0 %) isolates, with overall sensitivity and specificity rates >98 % and positive and negative predictive values >97 %. The most common AMR determinants were blaTEM-1, sul2, tet(A), strA-strB and floR. Phenotypic resistance to cefotaxime and azithromycin was low and observed in 6.2 % (151/2486) and 0.9 % (16/1834) of the isolates, respectively. Several multi-drug resistant NTS lineages were resistant to 3GC due to different genetic mechanisms including blaCMY-2, blaCTX-M-55 or blaCTX-M-65. This study shows WGS can enhance existing AMR surveillance in NTS datasets routinely produced in public health laboratories to identify emerging AMR in NTS. These approaches will be critical for developing capacity to detect emerging public health threats such as resistance to 3GC.
Collapse
Affiliation(s)
- Cheryll M. Sia
- Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia,*Correspondence: Cheryll M. Sia,
| | - Sarah L. Baines
- Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Mary Valcanis
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Darren Y. J. Lee
- Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Anders Gonçalves da Silva
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Susan A. Ballard
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | | | - Torsten Seemann
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Benjamin P. Howden
- Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia,Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Danielle J. Ingle
- Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia,National Centre for Epidemiology and Population Health, The Australian National University, Canberra, Australia,*Correspondence: Danielle J. Ingle,
| | - Deborah A. Williamson
- Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia,Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia,Department of Microbiology, Royal Melbourne Hospital, Melbourne, Australia,*Correspondence: Deborah A. Williamson,
| |
Collapse
|
15
|
Ingle DJ, Ambrose RL, Baines SL, Duchene S, Gonçalves da Silva A, Lee DYJ, Jones M, Valcanis M, Taiaroa G, Ballard SA, Kirk MD, Howden BP, Pearson JS, Williamson DA. Evolutionary dynamics of multidrug resistant Salmonella enterica serovar 4,[5],12:i:- in Australia. Nat Commun 2021; 12:4786. [PMID: 34373455 PMCID: PMC8352879 DOI: 10.1038/s41467-021-25073-w] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Accepted: 07/20/2021] [Indexed: 02/07/2023] Open
Abstract
Salmonella enterica serovar 4,[5],12:i:- (Salmonella 4,[5],12:i:-) is a monophasic variant of Salmonella Typhimurium that has emerged as a global cause of multidrug resistant salmonellosis. We used Bayesian phylodynamics, genomic epidemiology, and phenotypic characterization to describe the emergence and evolution of Salmonella 4,[5],12:i:- in Australia. We show that the interruption of the genetic region surrounding the phase II flagellin, FljB, causing a monophasic phenotype, represents a stepwise evolutionary event through the accumulation of mobile resistance elements with minimal impairment to bacterial fitness. We identify three lineages with different population dynamics and discrete antimicrobial resistance profiles emerged, likely reflecting differential antimicrobial selection pressures. Two lineages are associated with travel to South-East Asia and the third lineage is endemic to Australia. Moreover antimicrobial-resistant Salmonella 4,[5],12:i- lineages efficiently infected and survived in host phagocytes and epithelial cells without eliciting significant cellular cytotoxicity, suggesting a suppression of host immune response that may facilitate the persistence of Salmonella 4,[5],12:i:-.
Collapse
Affiliation(s)
- Danielle J Ingle
- Research School of Population Health, Australian National University, Canberra, ACT, Australia.
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia.
- Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia.
| | - Rebecca L Ambrose
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Melbourne, VIC, Australia
- Department of Molecular and Translational Research, Monash University, Melbourne, VIC, Australia
- Department of Microbiology, Monash University, Melbourne, VIC, Australia
| | - Sarah L Baines
- Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Sebastian Duchene
- Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Anders Gonçalves da Silva
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Darren Y J Lee
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Miriam Jones
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Melbourne, VIC, Australia
- Department of Molecular and Translational Research, Monash University, Melbourne, VIC, Australia
- Department of Microbiology, Monash University, Melbourne, VIC, Australia
| | - Mary Valcanis
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - George Taiaroa
- Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Susan A Ballard
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Martyn D Kirk
- Research School of Population Health, Australian National University, Canberra, ACT, Australia
| | - Benjamin P Howden
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
- Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Jaclyn S Pearson
- Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Melbourne, VIC, Australia
- Department of Molecular and Translational Research, Monash University, Melbourne, VIC, Australia
- Department of Microbiology, Monash University, Melbourne, VIC, Australia
| | - Deborah A Williamson
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia.
- Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia.
- Department of Microbiology, Royal Melbourne Hospital, Melbourne, VIC, Australia.
| |
Collapse
|
16
|
McWhorter A, Owens J, Valcanis M, Olds L, Myers C, Smith I, Trott D, McLelland D. In vitro invasiveness and antimicrobial resistance of Salmonella enterica subspecies isolated from wild and captive reptiles. Zoonoses Public Health 2021; 68:402-412. [PMID: 33655685 DOI: 10.1111/zph.12820] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Revised: 01/29/2021] [Accepted: 02/06/2021] [Indexed: 01/02/2023]
Abstract
Reptiles are carriers of Salmonella and can intermittently shed bacteria in their faeces. Contact with snakes and lizards is a source of human salmonellosis. Here, two populations of reptiles, wild and captive were surveyed for Salmonella. One hundred thirty wild-caught reptiles were sampled for Salmonella including 2 turtle, 9 snake and 31 lizard species. Fifty-two of 130 (40%) animals were Salmonella positive: one of 5 (20%) turtles, 7 of 14 (50%) snakes and 44 of 111 (39.6%) lizards. One hundred twenty-two reptiles were sampled from a zoo collection including 1 turtle, 6 tortoise, 9 lizard, 14 snake and 1 crocodile species. Forty-two of 122 (34.4%) captive reptiles sampled were Salmonella positive. Salmonella was most commonly isolated from lizards and snakes. Fifteen serotypes were identified from zoo and 19 from wild-caught reptiles and most were members of subspecies enterica (I), salamae (II), arizonae (IIIa) or diarizonae (IIIb). Antimicrobial susceptibility testing was conducted on all Salmonella isolates; only two exhibited resistance, a Salmonella subsp. (II) ser. 21:z10 :z6 (Wandsbek) isolate cultured from a wild-caught reptile and a Salmonella Typhimurium DT120 isolated from a captive snake. The invasive capacity of reptile-associated Salmonella strains into cultured human intestinal epithelial (Caco2) and mouse macrophages cell lines (J774A.1) was also investigated. All isolates were invasive into both cell lines. Significant (P ≤ 0.001) variability in invasiveness into polarized Caco2 cells was observed. Salmonella Eastbourne exhibited the highest invasiveness into Caco2 cells and Salmonella Chester the lowest, with mean per cent recoveries of 19.99 ± 0.32 and 1.23 ± 0.30, respectively. Invasion into J774A.1 macrophages was also variable but was not significant. Salmonella subsp. II ser. 17:g,t:- (Bleadon) exhibited the highest invasiveness into J774A.1 with a mean per cent recovery of 10.19 ± 0.19. Thus, reptile-associated Salmonellae are likely to have different capacities to cause disease in humans.
Collapse
Affiliation(s)
- Andrea McWhorter
- School of Animal and Veterinary Sciences, University of Adelaide, Roseworthy, SA, Australia
| | - Jane Owens
- Faculty of Veterinary and Agricultural Science, University of Melbourne, Parkville, Vic., Australia
| | - Mary Valcanis
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, Microbiological Diagnostic Unit-Public Health Laboratory, University of Melbourne, Melbourne, Vic., Australia
| | - Liberty Olds
- Adelaide Zoo, Zoos South Australia, SA, Australia
| | - Cecilia Myers
- Dunkeld Pastoral Co Pty Ltd, Dunkeld, Vic., Australia
| | - Ian Smith
- Adelaide Zoo, Zoos South Australia, SA, Australia
| | - Darren Trott
- School of Animal and Veterinary Sciences, University of Adelaide, Roseworthy, SA, Australia
| | | |
Collapse
|
17
|
Veltman T, Jordan D, McDevitt CA, Bell J, Howden BP, Valcanis M, O'Dea M, Abraham S, Scott P, Kovac JH, Chia R, Combs B, Chousalkar K, Wilson T, Trott DJ. Absence of high priority critically important antimicrobial resistance in Salmonella sp. isolated from Australian commercial egg layer environments. Int J Food Microbiol 2021; 340:109042. [PMID: 33461002 DOI: 10.1016/j.ijfoodmicro.2021.109042] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Revised: 12/16/2020] [Accepted: 12/29/2020] [Indexed: 11/19/2022]
Abstract
The development of antimicrobial resistance in foodborne pathogens is a growing public health concern. This study was undertaken to determine the antimicrobial susceptibility of Salmonella enterica subspecies enterica isolated from the Australian commercial egg layer industry. S. enterica subspecies enterica (n=307) isolated from Australian commercial layer flock environments (2015-2018) were obtained from reference, research and State Government laboratories from six Australian states. All Salmonella isolates were serotyped. Antimicrobial susceptibility testing (AST) for 16 antimicrobial agents was performed by broth microdilution. Antimicrobial resistance genes and sequence types (STs) were identified in significant isolates by whole genome sequencing (WGS). Three main serotypes were detected, S. Typhimurium (n=61, 19.9%), S. Senftenburg (n=45, 14.7%) and S. Agona (n=37, 12.1%). AST showed 293/307 (95.4%) isolates were susceptible to all tested antimicrobial agents and all isolates were susceptible to amoxicillin-clavulanate, azithromycin, ceftiofur, ceftriaxone, ciprofloxacin, colistin, florfenicol, gentamicin, kanamycin and trimethoprim-sulfamethoxazole. Low levels of non-susceptibility were observed to streptomycin (2.3%, n=7), sulfisoxazole (2.0%, n=6), chloramphenicol (1.3%, n=4) and tetracycline (1.0%, n=3). Very low levels of non-susceptibility were observed to ampicillin (2/307; 0.7%) and cefoxitin (2/307; 0.7%). Two isolates (S. Havana and S. Montevideo), exhibited multidrug-resistant phenotypes to streptomycin, sulfisoxazole and tetracycline and possessed corresponding antimicrobial resistance genes (aadA4, aac(6')-Iaa, sul1, tetB). One S. Typhimurium isolate was resistant to ampicillin and tetracycline, and possessed both tetA and blaTEM-1B. WGS also identified these isolates as belonging to ST4 (S. Montevideo), ST578 (S. Havana) and ST19 (S. Typhimurium). The absence of resistance to highest priority critically important antimicrobials as well as the extremely low level of AMR generally among Australian commercial egg layer Salmonella isolates likely reflect Australia's conservative antimicrobial registration policy in food-producing animals and low rates of antimicrobial use within the industry.
Collapse
Affiliation(s)
- Tania Veltman
- Australian Centre for Antimicrobial Resistance Ecology, School of Animal and Veterinary Sciences, The University of Adelaide, Roseworthy, Australia; Research Centre for Infectious Diseases, School of Biological Sciences, The University of Adelaide, Adelaide, Australia
| | - David Jordan
- Department of Primary Industries, New South Wales Government, Wollongbar, Australia
| | - Christopher A McDevitt
- Australian Centre for Antimicrobial Resistance Ecology, School of Animal and Veterinary Sciences, The University of Adelaide, Roseworthy, Australia; Research Centre for Infectious Diseases, School of Biological Sciences, The University of Adelaide, Adelaide, Australia
| | - Jan Bell
- Australian Centre for Antimicrobial Resistance Ecology, School of Animal and Veterinary Sciences, The University of Adelaide, Roseworthy, Australia; Research Centre for Infectious Diseases, School of Biological Sciences, The University of Adelaide, Adelaide, Australia
| | - Benjamin P Howden
- Microbiological Diagnostic Unit Public Health Laboratory, The University of Melbourne, The Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Mary Valcanis
- Microbiological Diagnostic Unit Public Health Laboratory, The University of Melbourne, The Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Mark O'Dea
- Antimicrobial Resistance and Infectious Diseases Laboratory, College of Science, Health, Engineering and Education, Murdoch University, Murdoch, Australia
| | - Sam Abraham
- Antimicrobial Resistance and Infectious Diseases Laboratory, College of Science, Health, Engineering and Education, Murdoch University, Murdoch, Australia
| | | | - Jessica H Kovac
- Australian Centre for Antimicrobial Resistance Ecology, School of Animal and Veterinary Sciences, The University of Adelaide, Roseworthy, Australia
| | | | - Barry Combs
- OzFoodNet, Communicable Disease Control Directorate, Perth, Australia
| | - Kapil Chousalkar
- Australian Centre for Antimicrobial Resistance Ecology, School of Animal and Veterinary Sciences, The University of Adelaide, Roseworthy, Australia
| | | | - Darren J Trott
- Australian Centre for Antimicrobial Resistance Ecology, School of Animal and Veterinary Sciences, The University of Adelaide, Roseworthy, Australia.
| |
Collapse
|
18
|
Wallace RL, Bulach D, Valcanis M, Polkinghorne BG, Pingault N, Stylianopoulos A, Givney RC, Glass K, Kirka MD. Identification of the first erm(B)-positive Campylobacter jejuni and Campylobacter coli associated with novel multidrug resistance genomic islands in Australia. J Glob Antimicrob Resist 2020; 23:311-314. [PMID: 33010486 DOI: 10.1016/j.jgar.2020.09.009] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Revised: 07/29/2020] [Accepted: 09/03/2020] [Indexed: 01/02/2023] Open
Abstract
OBJECTIVES This report describes the first identification of two Campylobacter isolates harbouring erm(B) in Australia. METHODS Two erm(B)-positive isolates, Campylobacter coli 18V1065H1 and Campylobacter jejuni 19W1001H1, were isolated from diarrhoeal faecal samples from two travellers who had recently returned from Southeast Asia. Isolates underwent whole-genome sequencing using an Illumina NextSeq system and were analysed with the Nullarbor pipeline. Antimicrobial resistance genes were identified using AMRFinderPlus and sequence types (STs) were determined by multilocus sequence typing and the PubMLST Campylobacter jejuni/coli typing scheme. RESULTS Besideserm(B), C. jejuni 19W1001H1 possessed six other resistance genes [aad9, aadE, aph(3')-Illa, blaOXA-185, catA13 and tet(O)], the gyrA T86I mutation and the RE-CmeABC multidrug efflux pump variant. Campylobacter coli 18V1065H1 also possessed six resistance genes [aad9, aadE, aph(3')-IIIa, blaOXA-61, sat4 and tet(O)] in addition to erm(B); however, this isolate lacked genetic evidence for resistance to fluoroquinolones (no gyrA mutation). The erm(B) locus differed between isolates and neither was identical to previously identified erm(B) multidrug resistance genomic island (MDRGI) types. Both erm(B)-bearing isolates belonged to novel sequence types: ST9967 (C. jejuni 19W1001H1) and ST10161 (C. coli 18V1065H1). CONCLUSIONS This study detected the presence oferm(B) in Campylobacter for the first time in Australia. This novel mechanism of macrolide resistance is a major concern both for human and animal health and warrants close surveillance as macrolides are often the drug of choice for treating campylobacteriosis. The erm(B) gene is associated with several MDRGIs and dissemination of this resistance mechanism will likely limit treatment options for Campylobacter infections.
Collapse
Affiliation(s)
- Rhiannon L Wallace
- National Centre for Epidemiology and Population Health, The Australian National University, Canberra, Australian Capital Territory, Australia
| | - Dieter Bulach
- Melbourne Bioinformatics, The University of Melbourne, Melbourne, Victoria, Australia; Microbiological Diagnostic Unit Public Health Laboratory, The Peter Doherty Institute, Melbourne, Victoria, Australia
| | - Mary Valcanis
- Microbiological Diagnostic Unit Public Health Laboratory, The Peter Doherty Institute, Melbourne, Victoria, Australia
| | - Benjamin G Polkinghorne
- National Centre for Epidemiology and Population Health, The Australian National University, Canberra, Australian Capital Territory, Australia
| | | | | | | | - Kathryn Glass
- National Centre for Epidemiology and Population Health, The Australian National University, Canberra, Australian Capital Territory, Australia
| | - Martyn D Kirka
- National Centre for Epidemiology and Population Health, The Australian National University, Canberra, Australian Capital Territory, Australia.
| |
Collapse
|
19
|
Ingle DJ, Easton M, Valcanis M, Seemann T, Kwong JC, Stephens N, Carter GP, Gonçalves da Silva A, Adamopoulos J, Baines SL, Holt KE, Chow EPF, Fairley CK, Chen MY, Kirk MD, Howden BP, Williamson DA. Co-circulation of Multidrug-resistant Shigella Among Men Who Have Sex With Men in Australia. Clin Infect Dis 2020; 69:1535-1544. [PMID: 30615105 DOI: 10.1093/cid/ciz005] [Citation(s) in RCA: 65] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Accepted: 01/04/2019] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND In urban Australia, the burden of shigellosis is either in returning travelers from shigellosis-endemic regions or in men who have sex with men (MSM). Here, we combine genomic data with comprehensive epidemiological data on sexual exposure and travel to describe the spread of multidrug-resistant Shigella lineages. METHODS A population-level study of all cultured Shigella isolates in the state of Victoria, Australia, was undertaken from 1 January 2016 through 31 March 2018. Antimicrobial susceptibility testing, whole-genome sequencing, and bioinformatic analyses of 545 Shigella isolates were performed at the Microbiological Diagnostic Unit Public Health Laboratory. Risk factor data on travel and sexual exposure were collected through enhanced surveillance forms or by interviews. RESULTS Rates of antimicrobial resistance were high, with 17.6% (95/541) and 50.6% (274/541) resistance to ciprofloxacin and azithromycin, respectively. There were strong associations between antimicrobial resistance, phylogeny, and epidemiology. Specifically, 2 major MSM-associated lineages were identified: a Shigellasonnei lineage (n = 159) and a Shigella flexneri 2a lineage (n = 105). Of concern, 147/159 (92.4%) of isolates within the S. sonnei MSM-associated lineage harbored mutations associated with reduced susceptibility to recommended oral antimicrobials: namely, azithromycin, trimethoprim-sulfamethoxazole, and ciprofloxacin. Long-read sequencing demonstrated global dissemination of multidrug-resistant plasmids across Shigella species and lineages, but predominantly associated with MSM isolates. CONCLUSIONS Our contemporary data highlight the ongoing public health threat posed by resistant Shigella, both in Australia and globally. Urgent multidisciplinary public health measures are required to interrupt transmission and prevent infection.
Collapse
Affiliation(s)
- Danielle J Ingle
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne.,National Centre for Epidemiology and Population Health, The Australian National University, Canberra
| | - Marion Easton
- Victorian Department of Health and Human Services, Melbourne
| | - Mary Valcanis
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne
| | - Torsten Seemann
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne.,Melbourne Bioinformatics Group, Victoria, Australia.,Doherty Applied Microbial Genomics, Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Parkville, Australia
| | - Jason C Kwong
- Doherty Applied Microbial Genomics, Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Parkville, Australia
| | - Nicola Stephens
- Victorian Department of Health and Human Services, Melbourne
| | - Glen P Carter
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne.,Doherty Applied Microbial Genomics, Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Parkville, Australia
| | - Anders Gonçalves da Silva
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne
| | | | - Sarah L Baines
- Doherty Applied Microbial Genomics, Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Parkville, Australia
| | - Kathryn E Holt
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Australia.,London School of Hygiene and Tropical Medicine, United Kingdom
| | - Eric P F Chow
- Melbourne Sexual Health Centre, Alfred Health, Carlton.,Central Clinical School, Monash University, Melbourne, Australia
| | - Christopher K Fairley
- Melbourne Sexual Health Centre, Alfred Health, Carlton.,Central Clinical School, Monash University, Melbourne, Australia
| | - Marcus Y Chen
- Melbourne Sexual Health Centre, Alfred Health, Carlton.,Central Clinical School, Monash University, Melbourne, Australia
| | - Martyn D Kirk
- National Centre for Epidemiology and Population Health, The Australian National University, Canberra
| | - Benjamin P Howden
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne.,Doherty Applied Microbial Genomics, Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Parkville, Australia
| | - Deborah A Williamson
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne.,Doherty Applied Microbial Genomics, Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Parkville, Australia
| |
Collapse
|
20
|
Wallace RL, Bulach DM, Jennison AV, Valcanis M, McLure A, Smith JJ, Graham T, Saputra T, Firestone S, Symes S, Waters N, Stylianopoulos A, Kirk MD, Glass K. Molecular characterization of Campylobacter spp. recovered from beef, chicken, lamb and pork products at retail in Australia. PLoS One 2020; 15:e0236889. [PMID: 32730330 PMCID: PMC7392323 DOI: 10.1371/journal.pone.0236889] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Accepted: 07/15/2020] [Indexed: 02/02/2023] Open
Abstract
Australian rates of campylobacteriosis are among the highest in developed countries, yet only limited work has been done to characterize Campylobacter spp. in Australian retail products. We performed whole genome sequencing (WGS) on 331 C. coli and 285 C. jejuni from retail chicken meat, as well as beef, chicken, lamb and pork offal (organs). Campylobacter isolates were highly diverse, with 113 sequence types (STs) including 38 novel STs, identified from 616 isolates. Genomic analysis suggests very low levels (2.3-15.3%) of resistance to aminoglycoside, beta-lactam, fluoroquinolone, macrolide and tetracycline antibiotics. A majority (>90%) of isolates (52/56) possessing the fluoroquinolone resistance-associated T86I mutation in the gyrA gene belonged to ST860, ST2083 or ST7323. The 44 pork offal isolates were highly diverse, representing 33 STs (11 novel STs) and harboured genes associated with resistance to aminoglycosides, lincosamides and macrolides not generally found in isolates from other sources. Prevalence of multidrug resistant genotypes was very low (<5%), but ten-fold higher in C. coli than C. jejuni. This study highlights that Campylobacter spp. from retail products in Australia are highly genotypically diverse and important differences in antimicrobial resistance exist between Campylobacter species and animal sources.
Collapse
Affiliation(s)
- Rhiannon L. Wallace
- National Centre for Epidemiology and Population Health, The Australian National University, Canberra, Australian Capital Territory, Australia
| | - Dieter M. Bulach
- Melbourne Bioinformatics, The University of Melbourne, Melbourne, Victoria, Australia
- Microbiological Diagnostic Unit Public Health Laboratory, The Peter Doherty Institute, Melbourne, Victoria, Australia
| | - Amy V. Jennison
- Public Health Microbiology, Forensic and Scientific Services, Queensland Health, Brisbane, Queensland, Australia
| | - Mary Valcanis
- Microbiological Diagnostic Unit Public Health Laboratory, The Peter Doherty Institute, Melbourne, Victoria, Australia
| | - Angus McLure
- National Centre for Epidemiology and Population Health, The Australian National University, Canberra, Australian Capital Territory, Australia
| | - James J. Smith
- Food Safety Standards and Regulation, Health Protection Branch, Queensland Health, Brisbane, Queensland, Australia
| | - Trudy Graham
- Public Health Microbiology, Forensic and Scientific Services, Queensland Health, Brisbane, Queensland, Australia
| | - Themy Saputra
- New South Wales Food Authority, NSW Government, Sydney, New South Wales, Australia
| | - Simon Firestone
- Melbourne Veterinary School, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria, Australia
| | - Sally Symes
- Department of Health and Human Services, Victoria State Government, Melbourne, Victoria, Australia
| | - Natasha Waters
- ACT Government Analytical Laboratory, Australian Capital Territory Health Directorate, Canberra, Australian Capital Territory, Australia
| | - Anastasia Stylianopoulos
- Department of Health and Human Services, Victoria State Government, Melbourne, Victoria, Australia
| | - Martyn D. Kirk
- National Centre for Epidemiology and Population Health, The Australian National University, Canberra, Australian Capital Territory, Australia
| | - Kathryn Glass
- National Centre for Epidemiology and Population Health, The Australian National University, Canberra, Australian Capital Territory, Australia
| |
Collapse
|
21
|
Chung The H, Boinett C, Pham Thanh D, Jenkins C, Weill FX, Howden BP, Valcanis M, De Lappe N, Cormican M, Wangchuk S, Bodhidatta L, Mason CJ, Nguyen TNT, Ha Thanh T, Voong VP, Duong VT, Nguyen PHL, Turner P, Wick R, Ceyssens PJ, Thwaites G, Holt KE, Thomson NR, Rabaa MA, Baker S. Dissecting the molecular evolution of fluoroquinolone-resistant Shigella sonnei. Nat Commun 2019; 10:4828. [PMID: 31645551 PMCID: PMC6811581 DOI: 10.1038/s41467-019-12823-0] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Accepted: 09/25/2019] [Indexed: 02/08/2023] Open
Abstract
Shigella sonnei increasingly dominates the international epidemiological landscape of shigellosis. Treatment options for S. sonnei are dwindling due to resistance to several key antimicrobials, including the fluoroquinolones. Here we analyse nearly 400 S. sonnei whole genome sequences from both endemic and non-endemic regions to delineate the evolutionary history of the recently emergent fluoroquinolone-resistant S. sonnei. We reaffirm that extant resistant organisms belong to a single clonal expansion event. Our results indicate that sequential accumulation of defining mutations (gyrA-S83L, parC-S80I, and gyrA-D87G) led to the emergence of the fluoroquinolone-resistant S. sonnei population around 2007 in South Asia. This clone was then transmitted globally, resulting in establishments in Southeast Asia and Europe. Mutation analysis suggests that the clone became dominant through enhanced adaptation to oxidative stress. Experimental evolution reveals that under fluoroquinolone exposure in vitro, resistant S. sonnei develops further intolerance to the antimicrobial while the susceptible counterpart fails to attain complete resistance. Shigella sonnei is one of the main species causing shigellosis worldwide. Here the authors analyse nearly 400 S. sonnei genome sequences and carry out experimental evolution experiments to shed light into the evolutionary processes underlying the recent emergence of fluoroquinolone resistance in this pathogen.
Collapse
Affiliation(s)
- Hao Chung The
- The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Christine Boinett
- The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam.,Centre for Tropical Medicine and Global Health, Oxford University, Oxford, UK
| | - Duy Pham Thanh
- The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Claire Jenkins
- Gastrointestinal Bacterial Reference Unit, National Infection Service, Public Health England, London, UK
| | | | - Benjamin P Howden
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Australia
| | - Mary Valcanis
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Australia
| | - Niall De Lappe
- National Salmonella, Shigella, and Listeria monocytogenes Reference Laboratory, University Hospital Galway, Galway, Ireland
| | - Martin Cormican
- School of Medicine, National University of Ireland Galway, Galway, Ireland
| | - Sonam Wangchuk
- Public Health Laboratory, Department of Public Health, Ministry of Health, Royal Government of Bhutan, Thimphu, Bhutan
| | - Ladaporn Bodhidatta
- Department of Enteric Diseases, Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - Carl J Mason
- Department of Enteric Diseases, Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - To Nguyen Thi Nguyen
- The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Tuyen Ha Thanh
- The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Vinh Phat Voong
- The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Vu Thuy Duong
- The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Phu Huong Lan Nguyen
- The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam.,The Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam
| | - Paul Turner
- Centre for Tropical Medicine and Global Health, Oxford University, Oxford, UK.,Cambodia-Oxford Medical Research Unit, Angkor Hospital for Children, Siem Reap, Cambodia
| | - Ryan Wick
- Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, VIC, 3004, Australia
| | | | - Guy Thwaites
- The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam.,Centre for Tropical Medicine and Global Health, Oxford University, Oxford, UK
| | - Kathryn E Holt
- Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, VIC, 3004, Australia.,London School of Hygiene and Tropical Medicine, London, UK
| | - Nicholas R Thomson
- London School of Hygiene and Tropical Medicine, London, UK.,The Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK
| | - Maia A Rabaa
- The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam. .,Centre for Tropical Medicine and Global Health, Oxford University, Oxford, UK.
| | - Stephen Baker
- The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam.,Centre for Tropical Medicine and Global Health, Oxford University, Oxford, UK.,Cambridge Institute of Therapeutic Immunology and Infectious Disease, The Department of Medicine, University of Cambridge, Cambridge, UK
| |
Collapse
|
22
|
Ingle DJ, Gonçalves da Silva A, Valcanis M, Ballard SA, Seemann T, Jennison AV, Bastian I, Wise R, Kirk MD, Howden BP, Williamson DA. Emergence and divergence of major lineages of Shiga-toxin-producing Escherichia coli in Australia. Microb Genom 2019; 5. [PMID: 31107203 PMCID: PMC6562248 DOI: 10.1099/mgen.0.000268] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Shiga-toxin-producing Escherichia coli (STEC) infection is an important global cause of foodborne disease. To date however, genomics-based studies of STEC have been predominately focused upon STEC collected in the Northern Hemisphere. Here, we demonstrate the population structure of 485 STEC isolates in Australia, and show that several clonal groups (CGs) common to Australia were infrequently detected in a representative selection of contemporary STEC genomes from around the globe. Further, phylogenetic analysis demonstrated that lineage II of the global O157:H7 STEC was most prevalent in Australia, and was characterized by a frameshift mutation in flgF, resulting in the H-non-motile phenotype. Strong concordance between in silico and phenotypic serotyping was observed, along with concordance between in silico and conventional detection of stx genes. These data represent the most comprehensive STEC analysis from the Southern Hemisphere, and provide a framework for future national genomics-based surveillance of STEC in Australia.
Collapse
Affiliation(s)
- Danielle J. Ingle
- Microbiological Diagnostic Unit Public Health Laboratory at the University of Melbourne, The Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
- National Centre for Epidemiology and Population Health, The Australian National University, Canberra, Australia
| | - Anders Gonçalves da Silva
- Microbiological Diagnostic Unit Public Health Laboratory at the University of Melbourne, The Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Mary Valcanis
- Microbiological Diagnostic Unit Public Health Laboratory at the University of Melbourne, The Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Susan A. Ballard
- Microbiological Diagnostic Unit Public Health Laboratory at the University of Melbourne, The Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Torsten Seemann
- Microbiological Diagnostic Unit Public Health Laboratory at the University of Melbourne, The Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
- Melbourne Bioinformatics Group, Victoria, Australia
| | - Amy V. Jennison
- Public Health Microbiology, Forensic and Scientific Services, Queensland Department of Health, Queensland, Australia
| | | | - Rolf Wise
- SA Pathology, South Australia, Australia
| | - Martyn D. Kirk
- National Centre for Epidemiology and Population Health, The Australian National University, Canberra, Australia
| | - Benjamin P. Howden
- Microbiological Diagnostic Unit Public Health Laboratory at the University of Melbourne, The Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
- Doherty Applied Microbial Genomics, Department Microbiology and Immunology, The University of Melbourne, The Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Deborah A. Williamson
- Microbiological Diagnostic Unit Public Health Laboratory at the University of Melbourne, The Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
- *Correspondence: Deborah A. Williamson,
| |
Collapse
|
23
|
Malau E, Ford R, Valcanis M, Jennison AV, Mosse J, Bean D, Yoannes M, Pomat W, Horwood PF, Greenhill AR. Antimicrobial sensitivity trends and virulence genes in Shigella spp. from the Oceania region. Infect Genet Evol 2018; 64:52-56. [PMID: 29906636 DOI: 10.1016/j.meegid.2018.06.015] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Revised: 06/08/2018] [Accepted: 06/11/2018] [Indexed: 01/23/2023]
Abstract
Shigella is a common cause of diarrhoea in Papua New Guinea (PNG) and other Oceania countries. However, little is known about the strains causing infection. Archived Shigella isolates (n = 72) were obtained from research laboratories in PNG and reference laboratories in Australia. Shigella virulence genes were detected by PCR, and antimicrobial susceptibility was determined by disk diffusion. The ipaH virulence gene was present in all 72 isolates. The prevalence of other virulence genes was variable, with ial, invE, ipaBCD, sen/ospD3 and virF present in 60% of isolates and set1A and set1B genes present in 42% of isolates. Most S. flexneri isolates contained genes encoding enterotoxin 1 and/or enterotoxin 2. Resistance to antibiotics was common, with 51/72 isolates resistant to 2-4 antimicrobials. A greater proportion of bacteria isolated since 2010 (relative to pre-2010 isolates) were resistant to commonly used antibiotics such as ampicillin, chloramphenicol, tetracycline, and trimethoprim-sulfamethoxazole; suggesting that antimicrobial resistance (AMR) in Shigella is increasing over time in the Oceania region. There is a need for improved knowledge regarding Shigella circulation in the Oceania region and further monitoring of AMR patterns.
Collapse
Affiliation(s)
- Elisheba Malau
- School of Health and Life Sciences, Federation University Australia, Churchill, Australia.
| | - Rebecca Ford
- Papua New Guinea Institute of Medical Research, Goroka, Papua New Guinea,.
| | - Mary Valcanis
- Microbiological Diagnostic Unit Public Health Laboratory, Doherty Institute, Melbourne, Australia.
| | - Amy V Jennison
- Public Health Microbiology, Forensic and Scientific Services, Queensland Department of Health, Brisbane, Australia.
| | - Jenny Mosse
- School of Health and Life Sciences, Federation University Australia, Churchill, Australia.
| | - David Bean
- School of Health and Life Sciences, Federation University Australia, Churchill, Australia.
| | - Mition Yoannes
- Papua New Guinea Institute of Medical Research, Goroka, Papua New Guinea,.
| | - William Pomat
- Papua New Guinea Institute of Medical Research, Goroka, Papua New Guinea,.
| | - Paul F Horwood
- School of Health and Life Sciences, Federation University Australia, Churchill, Australia; Australian Institute of Tropical Health and Medicine, James Cook University, Cairns, Australia.
| | - Andrew R Greenhill
- School of Health and Life Sciences, Federation University Australia, Churchill, Australia.
| |
Collapse
|
24
|
Ford L, Wang Q, Stafford R, Ressler KA, Norton S, Shadbolt C, Hope K, Franklin N, Krsteski R, Carswell A, Carter GP, Seemann T, Howard P, Valcanis M, Castillo CFS, Bates J, Glass K, Williamson DA, Sintchenko V, Howden BP, Kirk MD. Seven Salmonella Typhimurium Outbreaks in Australia Linked by Trace-Back and Whole Genome Sequencing. Foodborne Pathog Dis 2018; 15:285-292. [PMID: 29638170 DOI: 10.1089/fpd.2017.2353] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Salmonella Typhimurium is a common cause of foodborne illness in Australia. We report on seven outbreaks of Salmonella Typhimurium multilocus variable-number tandem-repeat analysis (MLVA) 03-26-13-08-523 (European convention 2-24-12-7-0212) in three Australian states and territories investigated between November 2015 and March 2016. We identified a common egg grading facility in five of the outbreaks. While no Salmonella Typhimurium was detected at the grading facility and eggs could not be traced back to a particular farm, whole genome sequencing (WGS) of isolates from cases from all seven outbreaks indicated a common source. WGS was able to provide higher discriminatory power than MLVA and will likely link more Salmonella Typhimurium cases between states and territories in the future. National harmonization of Salmonella surveillance is important for effective implementation of WGS for Salmonella outbreak investigations.
Collapse
Affiliation(s)
- Laura Ford
- 1 National Centre for Epidemiology and Population Health, Research School of Population Health, The Australian National University , Canberra, Australia .,2 OzFoodNet, Health Protection Service , Population Health Protection and Prevention, ACT Health, Canberra, Australia
| | - Qinning Wang
- 3 Centre for Infectious Diseases and Microbiology Laboratory Services, Pathology West-Institute of Clinical Pathology and Medical Research , Sydney, Australia
| | - Russell Stafford
- 4 Communicable Diseases Branch, Prevention Division, Queensland Health , Brisbane, Australia
| | - Kelly-Anne Ressler
- 5 South Eastern Sydney Local Health District , NSW Health, Sydney, Australia
| | - Sophie Norton
- 6 Western Sydney Local Health District , NSW Health, Penrith, Australia
| | | | - Kirsty Hope
- 8 New South Wales Ministry of Health , Sydney, Australia
| | - Neil Franklin
- 8 New South Wales Ministry of Health , Sydney, Australia
| | - Radomir Krsteski
- 2 OzFoodNet, Health Protection Service , Population Health Protection and Prevention, ACT Health, Canberra, Australia
| | - Adrienne Carswell
- 2 OzFoodNet, Health Protection Service , Population Health Protection and Prevention, ACT Health, Canberra, Australia
| | - Glen P Carter
- 9 Doherty Applied Microbial Genomics, Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity , Melbourne, Australia
| | - Torsten Seemann
- 9 Doherty Applied Microbial Genomics, Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity , Melbourne, Australia
| | - Peter Howard
- 3 Centre for Infectious Diseases and Microbiology Laboratory Services, Pathology West-Institute of Clinical Pathology and Medical Research , Sydney, Australia
| | - Mary Valcanis
- 10 Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity , Melbourne, Australia
| | - Cristina Fabiola Sotomayor Castillo
- 3 Centre for Infectious Diseases and Microbiology Laboratory Services, Pathology West-Institute of Clinical Pathology and Medical Research , Sydney, Australia .,11 Sydney Medical School-Westmead, The University of Sydney , Sydney, Australia .,12 Instituto de Salud Publica , Facultad de Medicina, Universidad Austral de Chile, Valdivia, Chile .,13 Centre for Infectious Diseases and Microbiology-Public Health, Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney , Sydney, Australia
| | - John Bates
- 14 Public Health Microbiology , Public & Environmental Health, Forensic and Scientific Services, Health Support Queensland, Department of Health, Coopers Plains, Australia
| | - Kathryn Glass
- 1 National Centre for Epidemiology and Population Health, Research School of Population Health, The Australian National University , Canberra, Australia
| | - Deborah A Williamson
- 9 Doherty Applied Microbial Genomics, Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity , Melbourne, Australia .,10 Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity , Melbourne, Australia
| | - Vitali Sintchenko
- 3 Centre for Infectious Diseases and Microbiology Laboratory Services, Pathology West-Institute of Clinical Pathology and Medical Research , Sydney, Australia .,13 Centre for Infectious Diseases and Microbiology-Public Health, Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney , Sydney, Australia
| | - Benjamin P Howden
- 9 Doherty Applied Microbial Genomics, Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity , Melbourne, Australia .,10 Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity , Melbourne, Australia .,15 Infectious Diseases Department, Austin Health , Heidelberg, Australia
| | - Martyn D Kirk
- 1 National Centre for Epidemiology and Population Health, Research School of Population Health, The Australian National University , Canberra, Australia
| |
Collapse
|
25
|
Williamson DA, Lane CR, Easton M, Valcanis M, Strachan J, Veitch MG, Kirk MD, Howden BP. Increasing Antimicrobial Resistance in Nontyphoidal Salmonella Isolates in Australia from 1979 to 2015. Antimicrob Agents Chemother 2018; 62:e02012-17. [PMID: 29180525 PMCID: PMC5786757 DOI: 10.1128/aac.02012-17] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Accepted: 11/13/2017] [Indexed: 12/28/2022] Open
Abstract
Australia has high and increasing rates of salmonellosis. To date, the serovar distribution and associated antimicrobial resistance (AMR) patterns of nontyphoidal Salmonella enterica (NTS) in Australia have not been assessed. Such information provides critical knowledge about AMR in the food chain and informs decisions about public health. We reviewed longitudinal data on NTS in two Australian states over a 37-year period, between 1979 and 2015, and antimicrobial resistance since 1984. Overall, 17% of isolates were nonsusceptible to at least one antimicrobial, 4.9% were nonsusceptible to ciprofloxacin, and 0.6% were nonsusceptible to cefotaxime. In total, 2.5% of isolates were from invasive infections, with no significant difference in AMR profiles between invasive and noninvasive isolates. Most isolates with clinically relevant AMR profiles were associated with travel, particularly to Southeast Asia, with multiple "incursions" of virulent and resistant clones into Australia. Our findings represent the largest longitudinal surveillance system for NTS in Australia and provide valuable public health knowledge on the trends and distribution of AMR in NTS. Ongoing surveillance is critical to identify local emergence of resistant isolates.
Collapse
Affiliation(s)
- Deborah A Williamson
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, The University of Melbourne at The Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Courtney R Lane
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, The University of Melbourne at The Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Marion Easton
- Department of Health and Human Services, Victoria, Australia
| | - Mary Valcanis
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, The University of Melbourne at The Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Janet Strachan
- Department of Health and Human Services, Victoria, Australia
| | - Mark G Veitch
- Department of Health and Human Services, Tasmania, Australia
| | | | - Benjamin P Howden
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology, The University of Melbourne at The Doherty Institute for Infection and Immunity, Melbourne, Australia
| |
Collapse
|
26
|
Ford L, Carter GP, Wang Q, Seemann T, Sintchenko V, Glass K, Williamson DA, Howard P, Valcanis M, Castillo CFS, Sait M, Howden BP, Kirk MD. Incorporating Whole-Genome Sequencing into Public Health Surveillance: Lessons from Prospective Sequencing of Salmonella Typhimurium in Australia. Foodborne Pathog Dis 2018; 15:161-167. [PMID: 29336594 DOI: 10.1089/fpd.2017.2352] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
In Australia, the incidence of Salmonella Typhimurium has increased dramatically over the past decade. Whole-genome sequencing (WGS) is transforming public health microbiology, but poses challenges for surveillance. To compare WGS-based approaches with conventional typing for Salmonella surveillance, we performed concurrent WGS and multilocus variable-number tandem-repeat analysis (MLVA) of Salmonella Typhimurium isolates from the Australian Capital Territory (ACT) for a period of 5 months. We exchanged data via a central shared virtual machine and performed comparative genomic analyses. Epidemiological evidence was integrated with WGS-derived data to identify related isolates and sources of infection, and we compared WGS data for surveillance with findings from MLVA typing. We found that WGS data combined with epidemiological data linked an additional 9% of isolates to at least one other isolate in the study in contrast to MLVA and epidemiological data, and 19% more isolates than epidemiological data alone. Analysis of risk factors showed that in one WGS-defined cluster, human cases had higher odds of purchasing a single egg brand. While WGS was more sensitive and specific than conventional typing methods, we identified barriers to uptake of genomic surveillance around complexity of reporting of WGS results, timeliness, acceptability, and stability. In conclusion, WGS offers higher resolution of Salmonella Typhimurium laboratory surveillance than existing methods and can provide further evidence on sources of infection in case and outbreak investigations for public health action. However, there are several challenges that need to be addressed for effective implementation of genomic surveillance in Australia.
Collapse
Affiliation(s)
- Laura Ford
- 1 National Centre for Epidemiology and Population Health, Research School of Population Health, The Australian National University , Canberra, Australia .,2 OzFoodNet, Health Protection Service, Population Health Protection and Prevention , ACT Health, Canberra, Australia
| | - Glen P Carter
- 3 Doherty Applied Microbial Genomics, Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity , Melbourne, Australia
| | - Qinning Wang
- 4 Centre for Infectious Diseases and Microbiology Laboratory Services, Pathology West-Institute of Clinical Pathology and Medical Research , Sydney, Australia
| | - Torsten Seemann
- 3 Doherty Applied Microbial Genomics, Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity , Melbourne, Australia
| | - Vitali Sintchenko
- 4 Centre for Infectious Diseases and Microbiology Laboratory Services, Pathology West-Institute of Clinical Pathology and Medical Research , Sydney, Australia .,5 Centre for Infectious Diseases and Microbiology-Public Health, Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney , Sydney, Australia
| | - Kathryn Glass
- 1 National Centre for Epidemiology and Population Health, Research School of Population Health, The Australian National University , Canberra, Australia
| | - Deborah A Williamson
- 3 Doherty Applied Microbial Genomics, Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity , Melbourne, Australia .,6 Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity , Melbourne, Australia
| | - Peter Howard
- 4 Centre for Infectious Diseases and Microbiology Laboratory Services, Pathology West-Institute of Clinical Pathology and Medical Research , Sydney, Australia
| | - Mary Valcanis
- 6 Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity , Melbourne, Australia
| | - Cristina Fabiola Sotomayor Castillo
- 4 Centre for Infectious Diseases and Microbiology Laboratory Services, Pathology West-Institute of Clinical Pathology and Medical Research , Sydney, Australia .,5 Centre for Infectious Diseases and Microbiology-Public Health, Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney , Sydney, Australia .,7 Sydney Medical School-Westmead, The University of Sydney , Sydney, Australia .,8 Instituto de Salud Publica , Facultad de Medicina, Universidad Austral de Chile, Valdivia, Chile
| | - Michelle Sait
- 5 Centre for Infectious Diseases and Microbiology-Public Health, Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney , Sydney, Australia
| | - Benjamin P Howden
- 3 Doherty Applied Microbial Genomics, Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity , Melbourne, Australia .,6 Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity , Melbourne, Australia .,9 Infectious Diseases Department, Austin Health , Heidelberg, Australia
| | - Martyn D Kirk
- 1 National Centre for Epidemiology and Population Health, Research School of Population Health, The Australian National University , Canberra, Australia
| |
Collapse
|
27
|
Ingle DJ, Valcanis M, Kuzevski A, Tauschek M, Inouye M, Stinear T, Levine MM, Robins-Browne RM, Holt KE. Corrigendum: In silico serotyping of E. coli from short read data identifies limited novel O-loci but extensive diversity of O:H serotype combinations within and between pathogenic lineages. Microb Genom 2017; 3:e000109. [PMID: 29026653 PMCID: PMC5605953 DOI: 10.1099/mgen.0.000109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2017] [Accepted: 02/15/2017] [Indexed: 12/03/2022] Open
Affiliation(s)
- Danielle J Ingle
- 3Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria 3010, Australia.,2Centre for Systems Genomics, University of Melbourne, Parkville, Victoria 3010, Australia.,1Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Mary Valcanis
- 4Microbiological Diagnostic Unit Public Health Laboratory, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Victoria 3010, Australia
| | - Alex Kuzevski
- 4Microbiological Diagnostic Unit Public Health Laboratory, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Victoria 3010, Australia
| | - Marija Tauschek
- 1Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Michael Inouye
- 6Department of Medicine, University of Maryland School of Medicine, Baltimore, MD 21201, USA.,5School of BioSciences, University of Melbourne, Victoria 3010, Australia.,2Centre for Systems Genomics, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Tim Stinear
- 1Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Myron M Levine
- 6Department of Medicine, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Roy M Robins-Browne
- 7Murdoch Childrens Research Institute, Royal Children's Hospital, Victoria 3010, Australia.,1Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Kathryn E Holt
- 3Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria 3010, Australia.,2Centre for Systems Genomics, University of Melbourne, Parkville, Victoria 3010, Australia
| |
Collapse
|
28
|
Sparham SJ, Kwong JC, Valcanis M, Easton M, Trott DJ, Seemann T, Stinear TP, Howden BP. Emergence of multidrug resistance in locally-acquired human infections with Salmonella Typhimurium in Australia owing to a new clade harbouring bla CTX-M-9. Int J Antimicrob Agents 2017; 50:101-105. [PMID: 28476613 DOI: 10.1016/j.ijantimicag.2017.02.014] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2016] [Revised: 02/06/2017] [Accepted: 02/10/2017] [Indexed: 10/19/2022]
Abstract
Antimicrobial resistance in non-typhoidal Salmonella is a critical problem globally, with the emergence of resistance to third-generation cephalosporins (3GCs) a particular concern. The aim of this study was to use whole-genome sequencing (WGS) to characterise recently identified human and non-human isolates of 3GC-resistant Salmonella enterica subsp. enterica serovar Typhimurium from Australia. The Illumina NextSeq sequencing platform was used to determine the genome sequences of 78 S. Typhimurium definitive type 44 isolated in Australia between 1992 and 2016, including 31 3GC-resistant isolates. Phylogenetic and bioinformatics analyses were subsequently performed using a number of in silico tools. We report the emergence of 3GC resistance in locally-acquired Australian S. Typhimurium for the first time. Phenotypically resistant isolates of human and animal origin were geographically restricted and were found by WGS all to be closely related and to carry blaCTX-M-9. Dairy cattle were the suspected source based on geographical clustering of animal isolates, which were predominantly bovine in origin. In conclusion, locally-acquired human cases of S. Typhimurium carrying blaCTX-M-9 were identified that appear to be of bovine origin, raising concerns regarding the human impact of off-label use of ceftiofur in cattle.
Collapse
Affiliation(s)
- Sarah J Sparham
- Microbiological Diagnostic Unit Public Health Laboratory, Melbourne, VIC, Australia; Infectious Diseases Department, Austin Health, Heidelberg, VIC, Australia
| | - Jason C Kwong
- Microbiological Diagnostic Unit Public Health Laboratory, Melbourne, VIC, Australia; Infectious Diseases Department, Austin Health, Heidelberg, VIC, Australia; Doherty Applied Microbial Genomics, Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Parkville, VIC, Australia; Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Mary Valcanis
- Microbiological Diagnostic Unit Public Health Laboratory, Melbourne, VIC, Australia
| | - Marion Easton
- Department of Health and Human Services, Victorian Government, Australia
| | - Darren J Trott
- Australian Centre for Antimicrobial Resistance Ecology, School of Animal and Veterinary Sciences, The University of Adelaide, Roseworthy, SA, Australia
| | - Torsten Seemann
- Microbiological Diagnostic Unit Public Health Laboratory, Melbourne, VIC, Australia; Doherty Applied Microbial Genomics, Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Parkville, VIC, Australia; Melbourne Bioinformatics, The University of Melbourne, Carlton, VIC, Australia
| | - Timothy P Stinear
- Doherty Applied Microbial Genomics, Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Parkville, VIC, Australia; Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia
| | - Benjamin P Howden
- Microbiological Diagnostic Unit Public Health Laboratory, Melbourne, VIC, Australia; Infectious Diseases Department, Austin Health, Heidelberg, VIC, Australia; Doherty Applied Microbial Genomics, Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Parkville, VIC, Australia; Department of Microbiology and Immunology, The University of Melbourne at The Peter Doherty Institute for Infection and Immunity, Melbourne, VIC, Australia.
| |
Collapse
|
29
|
Saeidabadi MS, Nili H, Dadras H, Sharifiyazdi H, Connolly J, Valcanis M, Raidal S, Ghorashi SA. Evaluation of PCR and high-resolution melt curve analysis for differentiation of Salmonella isolates. Avian Pathol 2017; 46:319-331. [PMID: 28000500 DOI: 10.1080/03079457.2016.1268676] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Consumption of poultry products contaminated with Salmonella is one of the major causes of foodborne diseases worldwide and therefore detection and differentiation of Salmonella spp. in poultry is important. In this study, oligonucleotide primers were designed from hemD gene and a PCR followed by high-resolution melt (HRM) curve analysis was developed for rapid differentiation of Salmonella isolates. Amplicons of 228 bp were generated from 16 different Salmonella reference strains and from 65 clinical field isolates mainly from poultry farms. HRM curve analysis of the amplicons differentiated Salmonella isolates and analysis of the nucleotide sequence of the amplicons from selected isolates revealed that each melting curve profile was related to a unique DNA sequence. The relationship between reference strains and tested specimens was also evaluated using a mathematical model without visual interpretation of HRM curves. In addition, the potential of the PCR-HRM curve analysis was evaluated for genotyping of additional Salmonella isolates from different avian species. The findings indicate that PCR followed by HRM curve analysis provides a rapid and robust technique for genotyping of Salmonella isolates to determine the serovar/serotype.
Collapse
Affiliation(s)
- Mohammad Sadegh Saeidabadi
- a School of Veterinary Medicine , Shiraz University , Shiraz , Iran.,b School of Animal and Veterinary Sciences , Charles Sturt University , Wagga Wagga , Australia
| | - Hassan Nili
- a School of Veterinary Medicine , Shiraz University , Shiraz , Iran
| | | | | | - Joanne Connolly
- b School of Animal and Veterinary Sciences , Charles Sturt University , Wagga Wagga , Australia.,c Graham Centre for Agricultural Innovation (NSW Department of Primary Industries and Charles Sturt University) , Wagga Wagga , Australia
| | - Mary Valcanis
- d Department of Microbiology and Immunology , The University of Melbourne , Parkville , Australia
| | - Shane Raidal
- b School of Animal and Veterinary Sciences , Charles Sturt University , Wagga Wagga , Australia.,c Graham Centre for Agricultural Innovation (NSW Department of Primary Industries and Charles Sturt University) , Wagga Wagga , Australia
| | - Seyed Ali Ghorashi
- b School of Animal and Veterinary Sciences , Charles Sturt University , Wagga Wagga , Australia.,c Graham Centre for Agricultural Innovation (NSW Department of Primary Industries and Charles Sturt University) , Wagga Wagga , Australia
| |
Collapse
|
30
|
Tai AYC, Easton M, Encena J, Rotty J, Valcanis M, Howden BP, Slota-Kan S, Gregory J. A review of the public health management of shigellosis in Australia in the era of culture-independent diagnostic testing. Aust N Z J Public Health 2016; 40:588-591. [PMID: 27774718 DOI: 10.1111/1753-6405.12590] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Revised: 03/01/2016] [Accepted: 06/01/2016] [Indexed: 11/30/2022] Open
Abstract
OBJECTIVE To review the national case definition for shigellosis following the introduction of culture independent diagnostic testing by clinical laboratories and provide evidence to reform jurisdictional public health practices for the management shigellosis., . METHODS A review of all Australian jurisdictional public health guidelines for shigellosis was conducted. Victorian 2014 shigellosis data were analysed: demographics and risk factors for cases identified by conventional culture or culture-independent diagnostic methods were described. RESULTS There was considerable variation in reporting of cases to the National Notifiable Disease Surveillance System (NNDSS) by the eight Australian jurisdictions, with an array of classifications based on diagnostic testing methodologies. Analysis of Victorian 2014 shigellosis data found that culture positive cases were more likely to have reported men who have sex with men (MSM) as a risk factor than PCR positive only cases (p<0.0001) and less likely to have reported overseas travel during their incubation period (p<0.0001). Over a 10-year period (2005 to 2014), only two of 86 cases who were employed in high-risk occupations had ongoing positive faecal cultures after appropriate treatment. CONCLUSIONS The national surveillance case definition for shigellosis should be reviewed to facilitate standardised reporting across Australia. All jurisdictions must consider the public health significance of PCR positive only results in their surveillance risk assessments to inform management of shigellosis cases.
Collapse
Affiliation(s)
- Alex Y C Tai
- Communicable Diseases Prevention & Control, Department of Health & Human Services, Victoria.,Infectious Diseases Department, Austin Health, Victoria
| | - Marion Easton
- Communicable Diseases Epidemiology & Surveillance and OzFoodNet, Department of Health & Human Services, Victoria
| | - Jess Encena
- Communicable Diseases Prevention & Control, Department of Health & Human Services, Victoria
| | - Jessica Rotty
- Communicable Diseases Prevention & Control, Department of Health & Human Services, Victoria
| | - Mary Valcanis
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, The Doherty Institute for Infection and Immunity, The University of Melbourne, Victoria
| | - Benjamin P Howden
- Infectious Diseases Department, Austin Health, Victoria.,Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, The Doherty Institute for Infection and Immunity, The University of Melbourne, Victoria
| | - Simon Slota-Kan
- Communicable Diseases Prevention & Control, Department of Health & Human Services, Victoria
| | - Joy Gregory
- Communicable Diseases Epidemiology & Surveillance and OzFoodNet, Department of Health & Human Services, Victoria
| |
Collapse
|
31
|
Chung The H, Rabaa MA, Pham Thanh D, De Lappe N, Cormican M, Valcanis M, Howden BP, Wangchuk S, Bodhidatta L, Mason CJ, Nguyen Thi Nguyen T, Vu Thuy D, Thompson CN, Phu Huong Lan N, Voong Vinh P, Ha Thanh T, Turner P, Sar P, Thwaites G, Thomson NR, Holt KE, Baker S. South Asia as a Reservoir for the Global Spread of Ciprofloxacin-Resistant Shigella sonnei: A Cross-Sectional Study. PLoS Med 2016; 13:e1002055. [PMID: 27483136 PMCID: PMC4970813 DOI: 10.1371/journal.pmed.1002055] [Citation(s) in RCA: 67] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/13/2015] [Accepted: 05/18/2016] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Antimicrobial resistance is a major issue in the Shigellae, particularly as a specific multidrug-resistant (MDR) lineage of Shigella sonnei (lineage III) is becoming globally dominant. Ciprofloxacin is a recommended treatment for Shigella infections. However, ciprofloxacin-resistant S. sonnei are being increasingly isolated in Asia and sporadically reported on other continents. We hypothesized that Asia is a primary hub for the recent international spread of ciprofloxacin-resistant S. sonnei. METHODS AND FINDINGS We performed whole-genome sequencing on a collection of 60 contemporaneous ciprofloxacin-resistant S. sonnei isolated in four countries within Asia (Vietnam, n = 11; Bhutan, n = 12; Thailand, n = 1; Cambodia, n = 1) and two outside of Asia (Australia, n = 19; Ireland, n = 16). We reconstructed the recent evolutionary history of these organisms and combined these data with their geographical location of isolation. Placing these sequences into a global phylogeny, we found that all ciprofloxacin-resistant S. sonnei formed a single clade within a Central Asian expansion of lineage III. Furthermore, our data show that resistance to ciprofloxacin within S. sonnei may be globally attributed to a single clonal emergence event, encompassing sequential gyrA-S83L, parC-S80I, and gyrA-D87G mutations. Geographical data predict that South Asia is the likely primary source of these organisms, which are being regularly exported across Asia and intercontinentally into Australia, the United States and Europe. Our analysis was limited by the number of S. sonnei sequences available from diverse geographical areas and time periods, and we cannot discount the potential existence of other unsampled reservoir populations of antimicrobial-resistant S. sonnei. CONCLUSIONS This study suggests that a single clone, which is widespread in South Asia, is likely driving the current intercontinental surge of ciprofloxacin-resistant S. sonnei and is capable of establishing endemic transmission in new locations. Despite being limited in geographical scope, our work has major implications for understanding the international transfer of antimicrobial-resistant pathogens, with S. sonnei acting as a tractable model for studying how antimicrobial-resistant Gram-negative bacteria spread globally.
Collapse
Affiliation(s)
- Hao Chung The
- The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Maia A. Rabaa
- The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
- Centre for Tropical Medicine and Global Health, Oxford University, Oxford, United Kingdom
| | - Duy Pham Thanh
- The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Niall De Lappe
- National Salmonella, Shigella, and Listeria monocytogenes Reference Laboratory, University Hospital Galway, Galway, Ireland
| | - Martin Cormican
- School of Medicine, National University of Ireland Galway, Galway, Ireland
| | - Mary Valcanis
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Australia
| | - Benjamin P. Howden
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Australia
| | - Sonam Wangchuk
- Public Health Laboratory, Department of Public Health, Ministry of Health, Royal Government of Bhutan, Thimphu, Bhutan
| | - Ladaporn Bodhidatta
- Department of Enteric Diseases, Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - Carl J. Mason
- Department of Enteric Diseases, Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - To Nguyen Thi Nguyen
- The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Duong Vu Thuy
- The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Corinne N. Thompson
- The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
- Centre for Tropical Medicine and Global Health, Oxford University, Oxford, United Kingdom
| | - Nguyen Phu Huong Lan
- The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
- The Hospital for Tropical Diseases, Ho Chi Minh City, Vietnam
| | - Phat Voong Vinh
- The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Tuyen Ha Thanh
- The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Paul Turner
- Centre for Tropical Medicine and Global Health, Oxford University, Oxford, United Kingdom
- Cambodia-Oxford Medical Research Unit, Angkor Hospital for Children, Siem Reap, Cambodia
| | - Poda Sar
- Cambodia-Oxford Medical Research Unit, Angkor Hospital for Children, Siem Reap, Cambodia
| | - Guy Thwaites
- The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
- Centre for Tropical Medicine and Global Health, Oxford University, Oxford, United Kingdom
| | - Nicholas R. Thomson
- The London School of Hygiene and Tropical Medicine, London, United Kingdom
- The Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, United Kingdom
| | - Kathryn E. Holt
- Centre for Systems Genomics, The University of Melbourne, Melbourne, Australia
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Melbourne, Australia
| | - Stephen Baker
- The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
- Centre for Tropical Medicine and Global Health, Oxford University, Oxford, United Kingdom
- The Wellcome Trust Sanger Institute, Hinxton, Cambridgeshire, United Kingdom
| |
Collapse
|
32
|
Ingle DJ, Valcanis M, Kuzevski A, Tauschek M, Inouye M, Stinear T, Levine MM, Robins-Browne RM, Holt KE. In silico serotyping of E. coli from short read data identifies limited novel O-loci but extensive diversity of O:H serotype combinations within and between pathogenic lineages. Microb Genom 2016; 2:e000064. [PMID: 28348859 PMCID: PMC5343136 DOI: 10.1099/mgen.0.000064] [Citation(s) in RCA: 81] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2016] [Accepted: 04/21/2016] [Indexed: 11/18/2022] Open
Abstract
The lipopolysaccharide (O) and flagellar (H) surface antigens of Escherichia coli are targets for serotyping that have traditionally been used to identify pathogenic lineages. These surface antigens are important for the survival of E. coli within mammalian hosts. However, traditional serotyping has several limitations, and public health reference laboratories are increasingly moving towards whole genome sequencing (WGS) to characterize bacterial isolates. Here we present a method to rapidly and accurately serotype E. coli isolates from raw, short read WGS data. Our approach bypasses the need for de novo genome assembly by directly screening WGS reads against a curated database of alleles linked to known and novel E. coli O-groups and H-types (the EcOH database) using the software package srst2. We validated the approach by comparing in silico results for 197 enteropathogenic E. coli isolates with those obtained by serological phenotyping in an independent laboratory. We then demonstrated the utility of our method to characterize isolates in public health and clinical settings, and to explore the genetic diversity of >1500 E. coli genomes from multiple sources. Importantly, we showed that transfer of O- and H-antigen loci between E. coli chromosomal backbones is common, with little evidence of constraints by host or pathotype, suggesting that E. coli ‘strain space’ may be virtually unlimited, even within specific pathotypes. Our findings show that serotyping is most useful when used in combination with strain genotyping to characterize microevolution events within an inferred population structure.
Collapse
Affiliation(s)
- Danielle J Ingle
- 2Centre for Systems Genomics, University of Melbourne, Parkville, Victoria 3010, Australia
- 1Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Parkville, Victoria 3010, Australia
- 3Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Mary Valcanis
- 4Microbiological Diagnostic Unit Public Health Laboratory, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Victoria 3010, Australia
| | - Alex Kuzevski
- 4Microbiological Diagnostic Unit Public Health Laboratory, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Victoria 3010, Australia
| | - Marija Tauschek
- 1Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Michael Inouye
- 2Centre for Systems Genomics, University of Melbourne, Parkville, Victoria 3010, Australia
- 5School of BioSciences, University of Melbourne, Victoria 3010, Australia
| | - Tim Stinear
- 1Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Myron M Levine
- 6Department of Medicine, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Roy M Robins-Browne
- 1Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Parkville, Victoria 3010, Australia
- 7Murdoch Childrens Research Institute, Royal Children's Hospital, Victoria 3010, Australia
| | - Kathryn E Holt
- 2Centre for Systems Genomics, University of Melbourne, Parkville, Victoria 3010, Australia
- 3Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria 3010, Australia
| |
Collapse
|
33
|
Lane CR, Sutton B, Valcanis M, Kirk M, Walker C, Lalor K, Stephens N. Travel Destinations and Sexual Behavior as Indicators of Antibiotic Resistant Shigella Strains--Victoria, Australia. Clin Infect Dis 2015; 62:722-729. [PMID: 26679624 DOI: 10.1093/cid/civ1018] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2015] [Accepted: 12/04/2015] [Indexed: 11/14/2022] Open
Abstract
BACKGROUND Knowledge of relationships between antibiotic susceptibility of Shigella isolates and travel destination or other risk factors can assist clinicians in determining appropriate antibiotic therapy prior to susceptibility testing. We describe relationships between resistance patterns and risk factors for acquisition in Shigella isolates using routinely collected data for notified cases of shigellosis between 2008 and 2012 in Victoria, Australia. METHODS We included all shigellosis patients notified during the study period, where Shigella isolates were tested for antimicrobial sensitivity using Clinical and Laboratory Standards Institute breakpoints. Cases were interviewed to collect data on risk factors, including recent travel. Data were analyzed using Stata 13.1 to examine associations between risk factors and resistant strains. RESULTS Of the 500 cases of shigellosis, 249 were associated with overseas travel and 210 were locally acquired. Forty-six of 51 isolates of Indian origin displayed decreased susceptibility or resistance to ciprofloxacin. All isolates of Indonesian origin were susceptible to ciprofloxacin. Twenty-six travel-related isolates were resistant to all tested oral antimicrobials. Male-to-male sexual contact was the primary risk factor for 80% (120/150) of locally acquired infections among adult males, characterized by distinct periodic Shigella sonnei outbreaks. CONCLUSIONS Clinicians should consider travel destination as a marker for resistance to common antimicrobials in returning travelers, where severe disease requires empirical treatment prior to receipt of individual sensitivity testing results. Repeated outbreaks of locally acquired shigellosis among men who have sex with men highlight the importance of prevention and control measures in this high-risk group.
Collapse
Affiliation(s)
- Courtney R Lane
- National Centre for Epidemiology and Population Health, Australian National University, Canberra
- Health Protection Branch, Victorian Department of Health and Human Services, Melbourne
- Microbiological Diagnostic Unit Public Health Laboratory, University of Melbourne, Australia
| | - Brett Sutton
- Health Protection Branch, Victorian Department of Health and Human Services, Melbourne
| | - Mary Valcanis
- Microbiological Diagnostic Unit Public Health Laboratory, University of Melbourne, Australia
| | - Martyn Kirk
- National Centre for Epidemiology and Population Health, Australian National University, Canberra
| | - Cathryn Walker
- Health Protection Branch, Victorian Department of Health and Human Services, Melbourne
| | - Karin Lalor
- Health Protection Branch, Victorian Department of Health and Human Services, Melbourne
| | - Nicola Stephens
- Health Protection Branch, Victorian Department of Health and Human Services, Melbourne
| |
Collapse
|
34
|
Baker KS, Dallman TJ, Ashton PM, Day M, Hughes G, Crook PD, Gilbart VL, Zittermann S, Allen VG, Howden BP, Tomita T, Valcanis M, Harris SR, Connor TR, Sintchenko V, Howard P, Brown JD, Petty NK, Gouali M, Thanh DP, Keddy KH, Smith AM, Talukder KA, Faruque SM, Parkhill J, Baker S, Weill FX, Jenkins C, Thomson NR. Intercontinental dissemination of azithromycin-resistant shigellosis through sexual transmission: a cross-sectional study. The Lancet Infectious Diseases 2015; 15:913-21. [DOI: 10.1016/s1473-3099(15)00002-x] [Citation(s) in RCA: 161] [Impact Index Per Article: 17.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
|
35
|
Wong VK, Baker S, Pickard DJ, Parkhill J, Page AJ, Feasey NA, Kingsley RA, Thomson NR, Keane JA, Weill FX, Edwards DJ, Hawkey J, Harris SR, Mather AE, Cain AK, Hadfield J, Hart PJ, Thieu NTV, Klemm EJ, Glinos DA, Breiman RF, Watson CH, Kariuki S, Gordon MA, Heyderman RS, Okoro C, Jacobs J, Lunguya O, Edmunds WJ, Msefula C, Chabalgoity JA, Kama M, Jenkins K, Dutta S, Marks F, Campos J, Thompson C, Obaro S, MacLennan CA, Dolecek C, Keddy KH, Smith AM, Parry CM, Karkey A, Mulholland EK, Campbell JI, Dongol S, Basnyat B, Dufour M, Bandaranayake D, Naseri TT, Singh SP, Hatta M, Newton P, Onsare RS, Isaia L, Dance D, Davong V, Thwaites G, Wijedoru L, Crump JA, De Pinna E, Nair S, Nilles EJ, Thanh DP, Turner P, Soeng S, Valcanis M, Powling J, Dimovski K, Hogg G, Farrar J, Holt KE, Dougan G. Phylogeographical analysis of the dominant multidrug-resistant H58 clade of Salmonella Typhi identifies inter- and intracontinental transmission events. Nat Genet 2015; 47:632-9. [PMID: 25961941 PMCID: PMC4921243 DOI: 10.1038/ng.3281] [Citation(s) in RCA: 298] [Impact Index Per Article: 33.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2014] [Accepted: 03/23/2015] [Indexed: 11/09/2022]
Abstract
The emergence of multidrug-resistant (MDR) typhoid is a major global health threat affecting many countries where the disease is endemic. Here whole-genome sequence analysis of 1,832 Salmonella enterica serovar Typhi (S. Typhi) identifies a single dominant MDR lineage, H58, that has emerged and spread throughout Asia and Africa over the last 30 years. Our analysis identifies numerous transmissions of H58, including multiple transfers from Asia to Africa and an ongoing, unrecognized MDR epidemic within Africa itself. Notably, our analysis indicates that H58 lineages are displacing antibiotic-sensitive isolates, transforming the global population structure of this pathogen. H58 isolates can harbor a complex MDR element residing either on transmissible IncHI1 plasmids or within multiple chromosomal integration sites. We also identify new mutations that define the H58 lineage. This phylogeographical analysis provides a framework to facilitate global management of MDR typhoid and is applicable to similar MDR lineages emerging in other bacterial species.
Collapse
Affiliation(s)
- Vanessa K Wong
- 1] Wellcome Trust Sanger Institute, Hinxton, UK. [2] Department of Microbiology, Addenbrooke's Hospital, Cambridge University Hospitals National Health Service (NHS) Foundation Trust, Cambridge, UK
| | - Stephen Baker
- 1] Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam. [2] Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, Oxford University, Oxford, UK. [3] Department of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | | | | | | | | | - Robert A Kingsley
- 1] Wellcome Trust Sanger Institute, Hinxton, UK. [2] Institute of Food Research, Norwich Research Park, Norwich, UK
| | - Nicholas R Thomson
- 1] Wellcome Trust Sanger Institute, Hinxton, UK. [2] Department of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK
| | | | | | - David J Edwards
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Melbourne, Victoria, Australia
| | - Jane Hawkey
- 1] Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Melbourne, Victoria, Australia. [2] Faculty of Veterinary and Agricultural Sciences, University of Melbourne, Melbourne, Victoria, Australia
| | | | | | - Amy K Cain
- Wellcome Trust Sanger Institute, Hinxton, UK
| | | | - Peter J Hart
- Institute of Biomedical Research, School of Immunity and Infection, College of Medicine and Dental Sciences, University of Birmingham, Birmingham, UK
| | - Nga Tran Vu Thieu
- Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | | | | | - Robert F Breiman
- 1] Kenya Medical Research Institute (KEMRI), Nairobi, Kenya. [2] Centers for Disease Control and Prevention, Atlanta, Georgia, USA. [3] Emory Global Health Institute, Atlanta, Georgia, USA
| | - Conall H Watson
- Centre for the Mathematical Modelling of Infectious Diseases, Department of Infectious Disease Epidemiology, London School of Hygiene and Tropical Medicine, London, UK
| | - Samuel Kariuki
- 1] Wellcome Trust Sanger Institute, Hinxton, UK. [2] Kenya Medical Research Institute (KEMRI), Nairobi, Kenya
| | - Melita A Gordon
- Institute of Infection and Global Health, University of Liverpool, Liverpool, UK
| | - Robert S Heyderman
- Malawi-Liverpool Wellcome Trust Clinical Research Programme, College of Medicine, University of Malawi, Blantyre, Malawi
| | | | - Jan Jacobs
- 1] Department of Clinical Sciences, Institute of Tropical Medicine, Antwerp, Belgium. [2] Department of Microbiology and Immunology, Katholieke Universiteit (KU) Leuven, University of Leuven, Leuven, Belgium
| | - Octavie Lunguya
- 1] National Institute for Biomedical Research, Kinshasa, Democratic Republic of the Congo. [2] University Hospital of Kinshasa, Kinshasa, Democratic Republic of the Congo
| | - W John Edmunds
- Centre for the Mathematical Modelling of Infectious Diseases, Department of Infectious Disease Epidemiology, London School of Hygiene and Tropical Medicine, London, UK
| | - Chisomo Msefula
- 1] Malawi-Liverpool Wellcome Trust Clinical Research Programme, College of Medicine, University of Malawi, Blantyre, Malawi. [2] Microbiology Department, College of Medicine, University of Malawi, Blantyre, Malawi
| | - Jose A Chabalgoity
- Departamento de Desarrollo Biotecnológico, Instituto de Higiene, Facultad de Medicina, Montevideo, Uruguay
| | | | | | - Shanta Dutta
- National Institute of Cholera and Enteric Diseases, Kolkata, India
| | - Florian Marks
- International Vaccine Institute, Department of Epidemiology, Seoul, Republic of Korea
| | - Josefina Campos
- Enteropathogen Division, Administración Nacional de Laboratorios e Institutos de Salud (ANLIS) Carlos G. Malbran Institute, Buenos Aires, Argentina
| | - Corinne Thompson
- 1] Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam. [2] Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, Oxford University, Oxford, UK
| | - Stephen Obaro
- 1] Division of Pediatric Infectious Diseases, University of Nebraska Medical Center, Omaha, Nebraska, USA. [2] University of Abuja Teaching Hospital, Abuja, Nigeria. [3] Bingham University, Karu, Nigeria
| | - Calman A MacLennan
- 1] Wellcome Trust Sanger Institute, Hinxton, UK. [2] Institute of Biomedical Research, School of Immunity and Infection, College of Medicine and Dental Sciences, University of Birmingham, Birmingham, UK. [3] Novartis Vaccines Institute for Global Health, Siena, Italy
| | - Christiane Dolecek
- Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, Oxford University, Oxford, UK
| | - Karen H Keddy
- Centre for Enteric Diseases, National Institute for Communicable Diseases, Division in the National Health Laboratory Service, University of the Witwatersrand, Johannesburg, South Africa
| | - Anthony M Smith
- Centre for Enteric Diseases, National Institute for Communicable Diseases, Division in the National Health Laboratory Service, University of the Witwatersrand, Johannesburg, South Africa
| | - Christopher M Parry
- 1] Department of Clinical Research, London School of Hygiene and Tropical Medicine, London, UK. [2] Graduate School of Tropical Medicine and Global Health, Nagasaki University, Nagasaki, Japan
| | - Abhilasha Karkey
- Patan Academy of Health Sciences, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Kathmandu, Nepal
| | - E Kim Mulholland
- 1] Department of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK. [2] Murdoch Childrens Research Institute, Melbourne, Victoria, Australia
| | - James I Campbell
- 1] Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam. [2] Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, Oxford University, Oxford, UK
| | - Sabina Dongol
- Patan Academy of Health Sciences, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Kathmandu, Nepal
| | - Buddha Basnyat
- Patan Academy of Health Sciences, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Kathmandu, Nepal
| | - Muriel Dufour
- Enteric and Leptospira Reference Laboratory, Institute of Environmental Science and Research, Ltd. (ESR), Porirua, New Zealand
| | - Don Bandaranayake
- National Centre for Biosecurity and Infectious Disease, Institute of Environmental Science and Research, Porirua, New Zealand
| | | | - Shalini Pravin Singh
- National Influenza Center, World Health Organization, Center for Communicable Disease Control, Suva, Fiji
| | - Mochammad Hatta
- Department of Microbiology, Hasanuddin University, Makassar, Indonesia
| | - Paul Newton
- 1] Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, Oxford University, Oxford, UK. [2] Lao Oxford Mahosot Wellcome Trust Research Unit, Microbiology Laboratory, Mahosot Hospital, Vientiane, Laos
| | | | | | - David Dance
- 1] Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, Oxford University, Oxford, UK. [2] Lao Oxford Mahosot Wellcome Trust Research Unit, Microbiology Laboratory, Mahosot Hospital, Vientiane, Laos
| | - Viengmon Davong
- Lao Oxford Mahosot Wellcome Trust Research Unit, Microbiology Laboratory, Mahosot Hospital, Vientiane, Laos
| | - Guy Thwaites
- 1] Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam. [2] Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, Oxford University, Oxford, UK
| | - Lalith Wijedoru
- 1] Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand. [2] Paediatric Emergency Medicine, Chelsea and Westminster Hospital, London, UK
| | - John A Crump
- Centre for International Health and Otago International Health Research Network, Dunedin School of Medicine, University of Otago, Dunedin, New Zealand
| | - Elizabeth De Pinna
- Salmonella Reference Service, Public Health England, Colindale, London, UK
| | - Satheesh Nair
- Salmonella Reference Service, Public Health England, Colindale, London, UK
| | - Eric J Nilles
- Emerging Disease Surveillance and Response, Division of Pacific Technical Support, World Health Organization, Suva, Fiji
| | - Duy Pham Thanh
- Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Paul Turner
- 1] Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, Oxford University, Oxford, UK. [2] Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand. [3] Cambodia-Oxford Medical Research Unit, Angkor Hospital for Children, Siem Reap, Cambodia
| | - Sona Soeng
- Cambodia-Oxford Medical Research Unit, Angkor Hospital for Children, Siem Reap, Cambodia
| | - Mary Valcanis
- Microbiological Diagnostic Unit-Public Health Laboratory, Department of Microbiology and Immunology at the Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
| | - Joan Powling
- Microbiological Diagnostic Unit-Public Health Laboratory, Department of Microbiology and Immunology at the Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
| | - Karolina Dimovski
- Microbiological Diagnostic Unit-Public Health Laboratory, Department of Microbiology and Immunology at the Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
| | - Geoff Hogg
- Microbiological Diagnostic Unit-Public Health Laboratory, Department of Microbiology and Immunology at the Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Victoria, Australia
| | - Jeremy Farrar
- 1] Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam. [2] Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, Oxford University, Oxford, UK
| | - Kathryn E Holt
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Melbourne, Victoria, Australia
| | | |
Collapse
|
36
|
Trubiano JA, Lee JYH, Valcanis M, Gregory J, Sutton BA, Holmes NE. Non-O1, non-O139 Vibrio cholerae bacteraemia in an Australian population. Intern Med J 2015; 44:508-11. [PMID: 24816311 DOI: 10.1111/imj.12409] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2013] [Accepted: 12/16/2013] [Indexed: 11/27/2022]
Abstract
This retrospective case series identifies the largest cohort of non-O1, non-O139 Vibrio cholerae bacteraemia in an Australian population from 2000 to 2013. We examine the risk factors, epidemiology, clinical presentations and mortality of non-O1, non-O139 V. cholerae bacteraemia in Victoria and compare them with published cases in the literature. This case series highlights the pathogenic potential of non-O1, non-O139 V. cholerae and identifies possible associations with host (underlying chronic liver disease and malignancy) and environmental factors (contaminated water supply and raw seafood). Clinicians should be aware of the morbidity and mortality associated with invasive non-O1, non-O139 V. cholerae infections, particularly in immunocompromised patients.
Collapse
Affiliation(s)
- J A Trubiano
- Department of Infectious Diseases, Austin Health, Melbourne, Victoria, Australia; Communicable Disease Prevention and Control Section, Health Protection Branch, Victorian Government Department of Health, Melbourne, Victoria, Australia
| | | | | | | | | | | |
Collapse
|
37
|
Ahmed MU, Dunn L, Valcanis M, Hogg G, Ivanova EP. Double-locus sequence typing using porA and peb1A for epidemiological studies of Campylobacter jejuni. Foodborne Pathog Dis 2013; 11:194-9. [PMID: 24404778 DOI: 10.1089/fpd.2013.1634] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Campylobacter jejuni is the leading cause of foodborne bacterial gastroenteritis worldwide. Bacterial typing schemes play an important role in epidemiological investigations to trace the source and route of transmission of the infectious agent by identifying outbreak and differentiating among sporadic infections. In this study, a double-locus sequence typing (DLST) scheme for C. jejuni based on concatenated partial sequences of porA and peb1A genes is proposed. The DLST scheme was validated using 50 clinical and environmental C. jejuni strains isolated from human (C5, H, H15-H19), chicken (CH1-CH15), water (W2-W17), and ovine samples (OV1-OV6). The scheme was found to be highly discriminatory (discrimination index [DI]=0.964) and epidemiologically concordant based on C. jejuni strains studied. The DLST showed discriminatory power above 0.95 and excellent congruence to multilocus sequence typing and can be recommended as a rapid and low-cost typing scheme for epidemiological investigation of C. jejuni. It is suggested that the DLST scheme is suitable for identification of outbreak strains and differentiation of the sporadic infection strains.
Collapse
Affiliation(s)
- Monir U Ahmed
- 1 Faculty of Life and Social Sciences, Swinburne University of Technology , Victoria, Australia
| | | | | | | | | |
Collapse
|
38
|
Commons RJ, McBryde E, Valcanis M, Powling J, Street A, Hogg G. Twenty‐six years of enteric fever in Australia: an epidemiological analysis of antibiotic resistance. Med J Aust 2012; 196:332-6. [DOI: 10.5694/mja12.10082] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Affiliation(s)
- Robert J Commons
- Victorian Infectious Diseases Service, Royal Melbourne Hospital, Melbourne, VIC
| | - Emma McBryde
- Victorian Infectious Diseases Service, Royal Melbourne Hospital, Melbourne, VIC
| | - Mary Valcanis
- Microbiological Diagnostic Unit Public Health Laboratory, University of Melbourne, Melbourne, VIC
| | - Joan Powling
- Microbiological Diagnostic Unit Public Health Laboratory, University of Melbourne, Melbourne, VIC
| | - Alan Street
- Victorian Infectious Diseases Service, Royal Melbourne Hospital, Melbourne, VIC
| | - Geoff Hogg
- Microbiological Diagnostic Unit Public Health Laboratory, University of Melbourne, Melbourne, VIC
| |
Collapse
|
39
|
Moffatt CRM, Lafferty AR, Khan S, Krsteski R, Valcanis M, Powling J, Veitch M. Salmonella Rubislaw gastroenteritis linked to a pet lizard. Med J Aust 2010; 193:54-5. [PMID: 20618116 DOI: 10.5694/j.1326-5377.2010.tb03743.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2010] [Accepted: 04/29/2010] [Indexed: 11/17/2022]
|
40
|
Mickan L, Doyle R, Valcanis M, Dingle KE, Unicomb L, Lanser J. Multilocus sequence typing of Campylobacter jejuni isolates from New South Wales, Australia. J Appl Microbiol 2007; 102:144-52. [PMID: 17184329 DOI: 10.1111/j.1365-2672.2006.03049.x] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
AIMS Multilocus sequence typing (MLST) was used to examine the diversity and population structure of Campylobacter jejuni isolates associated with sporadic cases of gastroenteritis in Australia, and to compare these isolates with those from elsewhere. METHODS AND RESULTS A total of 153 Camp. jejuni isolates were genotyped. Forty sequence types (STs) were found, 19 of which were previously undescribed and 21 identified in other countries. The 19 newly described STs accounted for 43% of isolates, 16 of which were assigned to known clonal complexes. Eighty-eight percent of isolates were assigned to a total of 15 clonal complexes. Of these, four clonal complexes accounted for 60% of isolates. Three STs accounted for nearly 40% of all isolates and appeared to be endemic, while 21 STs were represented by more than one isolate. Seven infections were acquired during international travel, and the associated isolates all had different STs, three of which were exclusive to the travel-acquired cases. Comparison of serotypes among isolates from clonal complexes revealed further diversity. Eight serotypes were identified among isolates from more than one clonal complex, while isolates from six clonal complexes displayed serotypes not previously associated with those clonal complexes. CONCLUSIONS Multilocus sequence typing is a useful tool for the discrimination of subtypes and examination of the population structure of Camp. jejuni associated with sporadic infections. SIGNIFICANCE AND IMPACT OF THE STUDY This study highlights the genotypic diversity of Camp. jejuni in Australia, demonstrating that STs causing disease have both a global and a local distribution evident from the typing of domestically and internationally acquired Camp. jejuni isolates.
Collapse
Affiliation(s)
- L Mickan
- Infectious Diseases Laboratories, Institute of Medical and Veterinary Science, Adelaide, SA, Australia.
| | | | | | | | | | | |
Collapse
|
41
|
Nair GB, Safa A, Bhuiyan NA, Nusrin S, Murphy D, Nicol C, Valcanis M, Iddings S, Kubuabola I, Vally H. Isolation of Vibrio cholerae O1 strains similar to pre-seventh pandemic El Tor strains during an outbreak of gastrointestinal disease in an island resort in Fiji. J Med Microbiol 2006; 55:1559-1562. [PMID: 17030916 DOI: 10.1099/jmm.0.46734-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Five strains of Vibrio cholerae O1, one each from an Australian and a New Zealand tourist with gastrointestinal illness returning from an island resort in Fiji and the remaining three from water sources located in the same resort, were extensively characterized. Conventional phenotypic traits that are used for biotyping of O1 V. cholerae categorized all five strains as belonging to the El Tor biotype. Genetic screening of 11 regions that are associated with virulence in V. cholerae showed variable results. The absence of genes comprising Vibrio seventh pandemic island-I (VSP-I) and VSP-II in all the strains indicated that these strains were very similar to the pre-seventh pandemic V. cholerae O1 El Tor strains. The ctxAB genes were absent in all strains whereas orfU and zot were present in four strains, indicating that the strains were non-toxigenic. Four strains carried a truncated CTX prophage. Although epidemiological and molecular studies suggested that these strains did not cause cholera amongst tourists at the resort, their similarity to pre-seventh pandemic strains, their prior association with gastrointestinal illness and their presence in the island resort setting warrant more attention.
Collapse
Affiliation(s)
- G Balakrish Nair
- International Centre for Diarrhoeal Diseases Research, Bangladesh (ICDDR,B) Dhaka, Bangladesh
| | - Ashrafus Safa
- International Centre for Diarrhoeal Diseases Research, Bangladesh (ICDDR,B) Dhaka, Bangladesh
| | - N A Bhuiyan
- International Centre for Diarrhoeal Diseases Research, Bangladesh (ICDDR,B) Dhaka, Bangladesh
| | - Suraia Nusrin
- International Centre for Diarrhoeal Diseases Research, Bangladesh (ICDDR,B) Dhaka, Bangladesh
| | - Denise Murphy
- Public Health Microbiology, Queensland Health Scientific Services, Coopers Plains, Queensland, Australia
| | - Carolyn Nicol
- Institute of Environmental Science and Research Limited (ESR), Kenepuru Science Centre, Poriru, New Zealand
| | - Mary Valcanis
- Microbiological Diagnostic Unit Public Health Laboratory (MDUPHL), Department of Microbiology and Immunology, The University of Melbourne, Melbourne, Victoria, Australia
| | - Steven Iddings
- World Health Organization (WHO), South Pacific Office, Suva, Fiji
| | - Ili Kubuabola
- Fiji Centre for Communicable Disease Control, Mataika House, Suva, Fiji
| | - Hassan Vally
- National Centre for Epidemiology and Population Health, ANU College of Medicine and Health Sciences, The Australian National University, Canberra, Australian Capital Territory, Australia
- World Health Organization (WHO), South Pacific Office, Suva, Fiji
| |
Collapse
|
42
|
Unicomb LE, Ferguson J, Stafford RJ, Ashbolt R, Kirk MD, Becker NG, Patel MS, Gilbert GL, Valcanis M, Mickan L. Low-Level Fluoroquinolone Resistance among Campylobacter jejuni Isolates in Australia. Clin Infect Dis 2006; 42:1368-74. [PMID: 16619147 DOI: 10.1086/503426] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2005] [Accepted: 01/23/2006] [Indexed: 11/03/2022] Open
Abstract
BACKGROUND Ciprofloxacin-resistant Campylobacter jejuni isolates obtained from infected patients in Australia have not been detected in studies of isolates from specific geographic areas. The Australian government has prohibited the use of fluoroquinolone in food-producing animals. To assess the impact of this policy, we have examined the antimicrobial susceptibility of isolates from 5 Australian states. METHODS We conducted a period-prevalence survey of the susceptibility of C. jejuni isolates to 10 antimicrobial agents. C. jejuni isolates obtained from 585 patients from 5 Australian states (Queensland, South Australia, Tasmania, Victoria, and Western Australia) were identified by means of notifiable disease databases and were systematically selected from September 2001 to August 2002. RESULTS Among locally acquired infections, only 2% of isolates (range, 0%-8% in different states) were resistant to ciprofloxacin. The locally acquired isolates also exhibited resistance to sulfisoxazole (55%), ampicillin (46%), roxithromycin (38%), tetracycline (7%), nalidixic acid (6%), chloramphenicol (3%), erythromycin (3%), gentamicin (2%), and kanamycin (0.2%). Treatment with antimicrobial agents in the 4 weeks before onset was not associated with ciprofloxacin resistance. CONCLUSIONS The very low level of ciprofloxacin resistance in C. jejuni isolates likely reflects the success of Australia's policy of restricting use of fluoroquinolones in food-producing animals.
Collapse
Affiliation(s)
- Leanne E Unicomb
- OzFoodNet, Queensland Health, Archerfield, Queensland, Australia.
| | | | | | | | | | | | | | | | | | | |
Collapse
|
43
|
Sharma H, Unicomb L, Forbes W, Djordjevic S, Valcanis M, Dalton C, Ferguson J. Antibiotic resistance in Campylobacter jejuni isolated from humans in the Hunter Region, New South Wales. Commun Dis Intell Q Rep 2004; 27 Suppl:S80-8. [PMID: 12807280] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 03/03/2023]
Abstract
Campylobacter is a common cause of bacterial gastroenteritis in Australia. Antibiotic resistance among Campylobacter is an emerging problem in Europe and the United States of America. Monitoring may detect emerging resistance. Since there is no epidemiologically validated subtyping system for Campylobacter, antimicrobial resistance patterns may prove useful as an epidemiological marker. Campylobacter isolates from residents of the Hunter region were differentiated by PCR into two categories: C. jejuni and non-C. jejuni. Minimal inhibitory concentrations (MIC) were determined for 10 antibiotics using the National Committee for Clinical Laboratory Standards (NCCLS) agar dilution methodology. Risk factor information including travel history were obtained as part of a case-control study by conducting telephone interviews with infected individuals. Sixty-four per cent, 3.4 per cent, 3.4 per cent and 11.2 per cent of C. jejuni isolates were resistant to ampicillin (at MIC > 8 mg/L), erythromycin (> 8 mg/L), nalidixic acid (> 32 mg/L) and tetracycline (> 8 mg/L), respectively. A diverse pattern of antibiotic resistance ('resistotypes') was detected with some change occurring over time. Several possible clusters of Campylobacter infections were identified based on resistotype. Of seven infections acquired during overseas travel, 57 per cent (4/7) were resistant to more than one antibiotic class compared to 10 per cent (14/144) of locally-acquired isolates (p=0.004, Fisher exact). The potential usefulness of resistotyping as an epidemiological marker is worthy of further exploration.
Collapse
Affiliation(s)
- Hemant Sharma
- University of Newcastle and Hunter Area Pathology Service, Newcastle, New South Wales
| | | | | | | | | | | | | |
Collapse
|
44
|
Genobile D, Gaston J, Tallis GF, Gregory JE, Griffith JM, Valcanis M, Lightfoot D, Marshall JA. An outbreak of shigellosis in a child care centre. Commun Dis Intell Q Rep 2004; 28:225-9. [PMID: 15460959] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 04/30/2023]
Abstract
Outbreaks of shigellosis in child care are not commonly reported in Australia, however Shigella bacteria can easily spread in these settings. We report an outbreak of shigellosis in a child care centre and discuss the control measures implemented. This investigation identified 20 confirmed cases of Shigella sonnei biotype g and a further 47 probable cases in children and staff who attended a child care centre, and their household contacts. The investigation highlighted the importance of stringent control measures and protocols for dealing with outbreaks of Shigella and other enteric infections in the child care setting, and the importance of prompt notification by both doctors and child care centres, of suspected outbreaks.
Collapse
Affiliation(s)
- Dania Genobile
- Communicable Diseases Section, Department of Human Services, Melbourne, Victoria
| | | | | | | | | | | | | | | |
Collapse
|